Actually, WinRAR provides this option. You just need to enable it as in the following screenshot (I got here by right clicking a folder and clicking "Add to RAR..."):
You can get there by going to Advanced -> Set Password, entering your password, and clicking on "Encrypt file names". This will disallow you to even open the archive without the proper password.
The new version of WinRAR, 5.00, has introduced the new RAR5 archive format and this feature is one of many improvements:
Save identical files as references
If this option is enabled, WinRAR analyzes the file contents before starting archiving. If several identical files larger than 64 KB are found, the first file in the set is saved as usual file and all following files are saved as references to this first file. It allows to reduce the archive size, but applies some restrictions to resulting archive. You must not delete or rename the first identical file in archive after the archive was created, because it will make extraction of following files using it as a reference impossible. If you modify the first file, following files will also have the modified contents after extracting. Extraction command must involve the first file to create following files successfully.
It is recommended to use this option only if you compress a lot of identical files, will not modify an archive later and will extract an archive entirely, without necessity to unpack or skip individual files. If all identical files are small enough to fit into compression dictionary, solid archiving can provide more flexible solution than this option.
Supported for RAR 5.0 archives only.
My quick test on a folder that contains 320,000 files (Baldur's Gate Trilogy with a lot of mods):
RAR4 compression method, compression set to "Store": 26.1 GB (28,053,815,768 bytes)
RAR5 compression method, compression set to "Store" and "Save identical files as references" turned on: 23.9 GB (25,722,664,097 bytes)
So I was able to save over 9% without using any compression at all!
Best Answer
use 7-zip to extract them directly (don't use a file joiner)
Unlike Winrar , 7-zip can handle those .001 type files.If one of the archive is corrupt it will surely mention the part ( " crc failed in part x " ) but this will occur only if the data is damaged during downloading .
If this is not the case you can only solve this with the help of a recovery record. Simplest way is ask the person who uploaded the files to give you each file's checksumthen compare each of your own file's checksum with it the file with a different checksum is corrupted.