Re-encoding in FFMPEG using the exact same settings as the input file

I have a use-case where I take a few MPEG-4 files, trim them and concatenate them in to one file.
I have a second use-case where one of those files are trimmed and also cropped/scaled, these files must be re-encoded.

The problem with the second use-case is that I end up with a mix of two different file layouts:

Trim only:

Format                         : MPEG-4
Format                         : AVC
Format/Info                    : Advanced Video Codec
Format profile                 : Main@L4.1
Format settings, CABAC         : Yes
Format settings, ReFrames      : 4 frames
Codec ID                       : avc1
Codec ID/Info                  : Advanced Video Coding
Duration                       : 28s 17ms
Bit rate                       : 3 362 Kbps
Width                          : 1 280 pixels
Height                         : 720 pixels
Display aspect ratio           : 16:9
Frame rate mode                : Variable
Frame rate                     : 60.000 fps
Minimum frame rate             : 58.824 fps
Maximum frame rate             : 62.500 fps
Color space                    : YUV
Chroma subsampling             : 4:2:0
Bit depth                      : 8 bits
Scan type                      : Progressive
Bits/(Pixel*Frame)             : 0.061
Stream size                    : 11.2 MiB (95%)
Color primaries                : BT.709
Transfer characteristics       : sYCC
Matrix coefficients            : BT.709

Trim + crop/scale(re-encode)

Format                         : MPEG-4
Format                         : AVC
Format/Info                    : Advanced Video Codec
Format profile                 : High 4:4:4 Predictive@L3.2
Format settings, CABAC         : No
Format settings, ReFrames      : 1 frame
Codec ID                       : avc1
Codec ID/Info                  : Advanced Video Coding
Duration                       : 29s 0ms
Bit rate                       : 24.8 Mbps
Width                          : 1 280 pixels
Height                         : 720 pixels
Display aspect ratio           : 16:9
Frame rate mode                : Constant
Frame rate                     : 60.000 fps
Color space                    : YUV
Chroma subsampling             : 4:2:0
Bit depth                      : 8 bits
Scan type                      : Progressive
Bits/(Pixel*Frame)             : 0.448
Stream size                    : 85.7 MiB (99%)
Writing library                : x264 core 144 r96 40bb568
Encoding settings              : cabac=0 / ref=1 / deblock=0:0:0 / analyse=0:0 / me=dia / subme=0 / psy=0 / mixed_ref=0 / me_range=16 / chroma_me=1 / trellis=0 / 8x8dct=0 / cqm=0 / deadzone=21,11 / fast_pskip=0 / chroma_qp_offset=0 / threads=3 / lookahead_threads=1 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=0 / weightp=0 / keyint=250 / keyint_min=25 / scenecut=0 / intra_refresh=0 / rc=cqp / mbtree=0 / qp=0

scale/crop command:

ffmpeg -i -ss 05 test.mp4 -c:a copy -vf "crop=w=(in_w/1000)*%d:h=(in_h/566)*%d:x=(in_w/1000)*%d:y=(in_h/566)*%d,scale=in_w:in_h" out-scale-crop.mp4

Per LordNeckbeard's request, FFMPEG's output has been added

ffmpeg version N-43527-gb23a866-   http://johnvansickle.com/ffmpeg/    Copyright (c) 2000-2015 the FFmpeg developers
  built on Jan 13 2015 01:29:05 with gcc 4.9.2 (Debian 4.9.2-10)
  configuration: --enable-gpl --enable-version3 --disable-shared --disable-debug --enable-runtime-cpudetect --enable-libmp3lame --enable-libx264 --enable-libx265 --enable-libwebp --enable-libspeex --enable-libvorbis --enable-libvpx --enable-libfreetype --enable-fontconfig --enable-libxvid --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-gray --enable-libopenjpeg --enable-libopus --disable-ffserver --enable-libass --enable-gnutls --cc=gcc
  libavutil      54. 16.100 / 54. 16.100
  libavcodec     56. 20.100 / 56. 20.100
  libavformat    56. 18.101 / 56. 18.101
  libavdevice    56.  4.100 / 56.  4.100
  libavfilter     5.  7.100 /  5.  7.100
  libswscale      3.  1.101 /  3.  1.101
  libswresample   1.  1.100 /  1.  1.100
  libpostproc    53.  3.100 / 53.  3.100
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/home/rohan/render_cache/v4033205_745.mp4':
  Metadata:
    major_brand     : isom
    minor_version   : 512
    compatible_brands: isomiso2avc1mp41
    encoder         : Lavf56.18.101
  Duration: 00:00:35.77, start: 0.000000, bitrate: 2143 kb/s
    Stream #0:0(und): Video: h264 (High) (avc1 / 0x31637661), yuv420p, 1920x1080, 2001 kb/s, 30 fps, 30 tbr, 90k tbn, 60 tbc (default)
    Metadata:
      handler_name    : VideoHandler
    Stream #0:1(und): Audio: aac (LC) (mp4a / 0x6134706D), 44100 Hz, stereo, fltp, 131 kb/s (default)
    Metadata:
      handler_name    : SoundHandler
[libx264 @ 0x360bd20] using cpu capabilities: MMX2 SSE Cache64
[libx264 @ 0x360bd20] profile High 4:4:4 Predictive, level 3.0, 4:2:0 8-bit
[libx264 @ 0x360bd20] 264 - core 144 r96 40bb568 - H.264/MPEG-4 AVC codec - Copyleft 2003-2014 - http://www.videolan.org/x264.html - options: cabac=0 ref=1 deblock=0:0:0 analyse=0:0 me=dia subme=0 psy=0 mixed_ref=0 me_range=16 chroma_me=1 trellis=0 8x8dct=0 cqm=0 deadzone=21,11 fast_pskip=0 chroma_qp_offset=0 threads=3 lookahead_threads=1 sliced_threads=0 nr=0 decimate=1 interlaced=0 bluray_compat=0 constrained_intra=0 bframes=0 weightp=0 keyint=250 keyint_min=25 scenecut=0 intra_refresh=0 rc=cqp mbtree=0 qp=0
Output #0, mp4, to '/home/rohan/render_cache/v4033205_745_1_cut.mp4':
  Metadata:
    major_brand     : isom
    minor_version   : 512
    compatible_brands: isomiso2avc1mp41
    encoder         : Lavf56.18.101
    Stream #0:0(und): Video: h264 (libx264) ([33][0][0][0] / 0x0021), yuv420p, 690x384, q=-1--1, 30 fps, 15360 tbn, 30 tbc (default)
    Metadata:
      handler_name    : VideoHandler
      encoder         : Lavc56.20.100 libx264
    Stream #0:1(und): Audio: aac ([64][0][0][0] / 0x0040), 44100 Hz, stereo, 131 kb/s (default)
    Metadata:
      handler_name    : SoundHandler
Stream mapping:
  Stream #0:0 -> #0:0 (h264 (native) -> h264 (libx264))
  Stream #0:1 -> #0:1 (copy)
Press [q] to stop, [?] for help
frame=   15 fps=0.0 q=0.0 size=     633kB time=00:00:00.55 bitrate=9409.0kbits/sframe=   65 fps= 65 q=0.0 size=    2986kB time=00:00:02.22 bitrate=11002.2kbits/frame=  117 fps= 77 q=0.0 size=    5507kB time=00:00:03.96 bitrate=11380.3kbits/frame=  182 fps= 91 q=0.0 size=    7832kB time=00:00:06.12 bitrate=10476.3kbits/frame=  244 fps= 97 q=0.0 size=   10248kB time=00:00:08.19 bitrate=10250.0kbits/frame=  290 fps= 96 q=0.0 size=   12275kB time=00:00:09.72 bitrate=10342.1kbits/frame=  337 fps= 96 q=0.0 size=   14408kB time=00:00:11.27 bitrate=10464.6kbits/frame=  401 fps= 99 q=0.0 size=   17318kB time=00:00:13.41 bitrate=10575.5kbits/frame=  458 fps=101 q=0.0 size=   20332kB time=00:00:15.31 bitrate=10872.8kbits/frame=  477 fps= 90 q=0.0 size=   21308kB time=00:00:15.94 bitrate=10946.6kbits/frame=  541 fps= 93 q=0.0 size=   24973kB time=00:00:18.08 bitrate=11314.0kbits/frame=  601 fps= 95 q=0.0 size=   28271kB time=00:00:20.07 bitrate=11534.2kbits/frame=  654 fps= 96 q=0.0 size=   31201kB time=00:00:21.84 bitrate=11701.2kbits/frame=  714 fps= 97 q=0.0 size=   34484kB time=00:00:23.86 bitrate=11837.8kbits/frame=  769 fps= 98 q=0.0 size=   37860kB time=00:00:25.69 bitrate=12069.0kbits/frame=  814 fps= 97 q=0.0 size=   40593kB time=00:00:27.18 bitrate=12232.8kbits/frame=  840 fps= 97 q=-1.0 Lsize=   42204kB time=00:00:28.02 bitrate=12338.7kbits/s dup=1 drop=0
video:41726kB audio:453kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.058509%
[libx264 @ 0x360bd20] frame I:4     Avg QP: 0.00  size:132759
[libx264 @ 0x360bd20] frame P:836   Avg QP: 0.00  size: 50474
[libx264 @ 0x360bd20] mb I  I16..4: 100.0%  0.0%  0.0%
[libx264 @ 0x360bd20] mb P  I16..4: 15.1%  0.0%  0.0%  P16..4: 40.7%  0.0%  0.0%  0.0%  0.0%    skip:44.2%
[libx264 @ 0x360bd20] coded y,uvDC,uvAC intra: 99.5% 98.9% 98.7% inter: 36.3% 39.9% 39.5%
[libx264 @ 0x360bd20] i16 v,h,dc,p: 56% 44%  0%  0%
[libx264 @ 0x360bd20] i8c dc,h,v,p:  0% 44% 55%  0%
[libx264 @ 0x360bd20] kb/s:12207.68

trim command:

ffmpeg -i -ss 05 test.mp4 -codec copy trimmed.mp4

ffmpeg version N-43527-gb23a866-   http://johnvansickle.com/ffmpeg/    Copyright (c) 2000-2015 the FFmpeg developers
  built on Jan 13 2015 01:29:05 with gcc 4.9.2 (Debian 4.9.2-10)
  configuration: --enable-gpl --enable-version3 --disable-shared --disable-debug --enable-runtime-cpudetect --enable-libmp3lame --enable-libx264 --enable-libx265 --enable-libwebp --enable-libspeex --enable-libvorbis --enable-libvpx --enable-libfreetype --enable-fontconfig --enable-libxvid --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-gray --enable-libopenjpeg --enable-libopus --disable-ffserver --enable-libass --enable-gnutls --cc=gcc
  libavutil      54. 16.100 / 54. 16.100
  libavcodec     56. 20.100 / 56. 20.100
  libavformat    56. 18.101 / 56. 18.101
  libavdevice    56.  4.100 / 56.  4.100
  libavfilter     5.  7.100 /  5.  7.100
  libswscale      3.  1.101 /  3.  1.101
  libswresample   1.  1.100 /  1.  1.100
  libpostproc    53.  3.100 / 53.  3.100
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/home/rohan/render_cache/v4033205_6295.mp4':
  Metadata:
    major_brand     : isom
    minor_version   : 512
    compatible_brands: isomiso2avc1mp41
    encoder         : Lavf56.18.101
  Duration: 00:00:36.02, start: 0.000000, bitrate: 2142 kb/s
    Stream #0:0(und): Video: h264 (High) (avc1 / 0x31637661), yuv420p, 1920x1080, 2001 kb/s, 30 fps, 30 tbr, 90k tbn, 60 tbc (default)
    Metadata:
      handler_name    : VideoHandler
    Stream #0:1(und): Audio: aac (LC) (mp4a / 0x6134706D), 44100 Hz, stereo, fltp, 131 kb/s (default)
    Metadata:
      handler_name    : SoundHandler
Output #0, mp4, to '/home/rohan/render_cache/v4033205_6295_0_cut.mp4':
  Metadata:
    major_brand     : isom
    minor_version   : 512
    compatible_brands: isomiso2avc1mp41
    encoder         : Lavf56.18.101
    Stream #0:0(und): Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 1920x1080, q=2-31, 2001 kb/s, 30 fps, 30 tbr, 90k tbn, 90k tbc (default)
    Metadata:
      handler_name    : VideoHandler
    Stream #0:1(und): Audio: aac ([64][0][0][0] / 0x0040), 44100 Hz, stereo, 131 kb/s (default)
    Metadata:
      handler_name    : SoundHandler
Stream mapping:
  Stream #0:0 -> #0:0 (copy)
  Stream #0:1 -> #0:1 (copy)
Press [q] to stop, [?] for help
frame=  841 fps=0.0 q=-1.0 Lsize=    7498kB time=00:00:28.02 bitrate=2192.1kbits/s

When I play these a set of trimmed files concatenated into one file, everything seems to playback correctly on MPC-HC and Youtube, but when I add in scaled/croppped files and concatenate those together with the non-scaled/cropped files both player freeze when switching to the next segments.

I suspect the variable/constant frame-rate switching being the culprit.

The easy solution would be to just re-encode everything to the same constant frame-rate, but I'm hoping I don't have to (codec: copy is fast and keeps the quality) and the source I'm receiving these files from could have different frame rates etc.

Preferably I'd like to perform the crop/scale re-encode using the exact same settings as the input file so I don't run into this mismatch in output files when concatenating. Is this possible?

Edit #2, @occvtech

I am indeed using the concat protocol using a merge_list.txt like so:

./ffmpeg -f concat -i merge_list.txt -codec copy output.mp4

And its output:

ffmpeg version 2.6.2-   http://johnvansickle.com/ffmpeg/    Copyright (c) 2000-2015 the FFmpeg developers
  built with gcc 4.9.2 (Debian 4.9.2-10)
  configuration: --enable-gpl --enable-version3 --disable-shared --disable-debug --enable-runtime-cpudetect --enable-libmp3lame --enable-libx264 --enable-libx265 --enable-libwebp --enable-libspeex --enable-libvorbis --enable-libvpx --enable-libfreetype --enable-fontconfig --enable-libxvid --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libtheora --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-gray --enable-libopenjpeg --enable-libopus --enable-libass --enable-gnutls --enable-libvidstab --enable-libsoxr --cc=gcc-4.9
  libavutil      54. 20.100 / 54. 20.100
  libavcodec     56. 26.100 / 56. 26.100
  libavformat    56. 25.101 / 56. 25.101
  libavdevice    56.  4.100 / 56.  4.100
  libavfilter     5. 11.102 /  5. 11.102
  libswscale      3.  1.101 /  3.  1.101
  libswresample   1.  1.100 /  1.  1.100
  libpostproc    53.  3.100 / 53.  3.100
Input #0, concat, from '/home/rohan/render_cache/merge_list.txt':
  Duration: N/A, start: 0.000000, bitrate: 2208 kb/s
    Stream #0:0: Video: h264 (High) (avc1 / 0x31637661), yuv420p, 1920x1080, 2076 kb/s, 30 fps, 30 tbr, 90k tbn, 60 tbc
    Stream #0:1: Audio: aac (LC) (mp4a / 0x6134706D), 44100 Hz, stereo, fltp, 131 kb/s
Output #0, mp4, to '/home/rohan/render_cache/sivhd_final.mp4':
  Metadata:
    encoder         : Lavf56.25.101
    Stream #0:0: Video: h264 ([33][0][0][0] / 0x0021), yuv420p, 1920x1080, q=2-31, 2076 kb/s, 30 fps, 30 tbr, 15360 tbn, 60 tbc
    Stream #0:1: Audio: aac ([64][0][0][0] / 0x0040), 44100 Hz, stereo, 131 kb/s
Stream mapping:
  Stream #0:0 -> #0:0 (copy)
  Stream #0:1 -> #0:1 (copy)
Press [q] to stop, [?] for help
[concat @ 0x3204d60] DTS 92955 < 541117 out of order
[mp4 @ 0x322eb80] Non-monotonous DTS in output stream 0:0; previous: 92351, current: 15864; changing to 92352. This may result in incorrect timestamps in the output file. x 2000

frame=  421 fps=0.0 q=-1.0 Lsize=   13507kB time=00:00:14.07 bitrate=7862.8kbits/s
video:13268kB audio:226kB subtitle:0kB other streams:0kB global headers:0kB muxing overhead: 0.096110%

The Non-monotonous DTS is warning is printed quite a lot(240 times), but DTS refers to audio and the audio in the output file sounds fine up until the croppped/trim part.

Also I have tried your suggestion to change the framerate (and combinations with different vsync parameters) both at the trim/crop ffmpeg step and the concat step but they only really seem to have effect when I'm re-encoding, not copy codeccing.

—

After I started writing this second edit, I been trying every vsync, filter:v fps, framerate, -r argument for a few hours now and the only actual working solution so far for has been re encoding everything with 60 fps(even if they are not trimmed/cropped) and concat-ing that. Using -preset ultrafast and -qp 0 it feels fast enough and the filesizes are quite big but I'm not keeping the files anyway.

So it seems codec copy is a no-go when there's at least one croppped/scaled file in there.

If anybody else does have a solution regarding this without needing to re-encode everything i'l gladly accept that otherwise I'l award the bounty to @occvtech.