MacOS – OSX High Sierra – Files and Folders show as empty/invisible in Finder, but are still there

I am running the latest version of High Sierra.

Both my user Library/Application Support and main Library/Application Support are completely empty when opened in Finder (see screenshot).

I was asked to delete a configuration file for an app I use which was misbehaving (a security-related app–a VPN app), and discovered that I cannot view files in these directories.

Yet, when I reinstalled the app, its configuration was still in place, meaning most likely that those folders DO still have their contents (which I have seen before) but they are being hidden from me.

Also I might add two things:

1) When this started happening two days ago, not only was that one folder empty in Finder (but not in Terminal), but since then, NO new files/folders created show up in Finder, and

2) If I kill Finder, and restart it, some of the new files show up. But it all started with that one folder; other pre-existing files and folders were not invisible-ized.

How can I fix this, and is it a hack? I am trying to run a VPN, after all.

The results of running cd ~/Library and `\ls -alt', as requested (and run as root, just for the sake of it).

root:/Users/myuser/Library |#\ls -alt
total 32
drwx------+ 561 myuser staff 17952 Nov 19 00:00 Preferences
drwxr-xr-x 40 myuser staff 1280 Nov 18 23:59 Safari
drwx------@ 43 myuser staff 1376 Nov 18 23:59 Cookies
drwxr-xr-x 30 myuser staff 960 Nov 18 23:58 SyncedPreferences
drwx------+ 7 myuser staff 224 Nov 18 23:51 Spelling
drwxr-xr-x 11 myuser staff 352 Nov 18 23:45 Assistant
drwx------+ 119 myuser staff 3808 Nov 18 23:40 Application Support
drwxr-xr-x 13 myuser staff 416 Nov 18 23:40 Keychains
drwx------+ 103 myuser staff 3296 Nov 18 23:39 Caches
drwxr-xr-x 5 myuser staff 160 Nov 18 23:34 Parallels
drwx------@ 49 myuser staff 1568 Nov 18 23:34 Saved Application State
drwxr-xr-x 10 myuser staff 320 Nov 18 00:14 Passes
drwxr-xr-x@ 66 myuser staff 2112 Nov 17 15:20 Mobile Documents
drwxr-xr-x@ 21 myuser staff 672 Nov 15 23:58 Suggestions
drwxr-xr-x 4 myuser staff 128 Nov 15 17:07 Google
drwxr-xr-x 3 myuser staff 96 Nov 14 12:50 CoreFollowUp
drwx------ 10 myuser staff 320 Nov 12 09:51 IdentityServices
drwxr-xr-x 25 myuser staff 800 Nov 12 09:50 Calendars
drwx------+ 122 myuser staff 3904 Nov 12 09:50 Logs
drwxr-xr-x@ 101 myuser staff 3232 Nov 12 09:33 ..
drwxr-xr-x 207 myuser staff 6624 Nov 8 10:01 Application Scripts
drwx------ 239 myuser staff 7648 Nov 8 10:01 Containers
drwx------ 23 myuser staff 736 Nov 8 10:01 Group Containers
drwxr-xr-x 2 myuser staff 64 Nov 7 18:45 PhotoshopCrashes
drwxr-xr-x 6 myuser staff 192 Oct 21 14:56 Keyboard
drwx------ 20 myuser staff 640 Oct 18 22:18 WebKit
drwxrwxrwx 4 myuser staff 128 Oct 15 01:25 Tokyo Dawn Labs
drwx------@ 90 myuser staff 2880 Oct 11 02:09 .
-rw-r--r-- 1 myuser staff 67 Oct 11 02:09 StickiesDatabase
drwx------+ 4 myuser staff 128 Sep 30 02:42 PreferencePanes
-rw-r--r--@ 1 myuser staff 6148 Sep 30 02:42 .DS_Store
drwxr-xr-x 3 myuser staff 96 Sep 27 15:49 com.apple.internal.ck
drwx------+ 5 myuser staff 160 Sep 27 13:57 Printers
drwx------@ 6 myuser staff 192 Sep 27 03:49 Mail
drwxr-xr-x@ 2 myuser staff 64 Sep 27 03:18 SafariSafeBrowsing
drwxr-xr-x 4 myuser staff 128 Sep 27 01:53 Metadata
drwxr-xr-x 3 myuser staff 96 Sep 27 01:50 FileProvider
drwx------ 7 myuser staff 224 Sep 27 01:50 Messages
drwx------ 8 myuser staff 256 Sep 27 01:50 Accounts
drwxr-xr-x 3 myuser staff 96 Sep 27 01:50 Family
drwxr-xr-x 24 myuser staff 768 Sep 6 15:40 SafariTechnologyPreview
drwx------ 5 myuser staff 160 Sep 1 19:01 Autosave Information
drwxr-xr-x 4 myuser staff 128 Sep 1 18:56 Scripts
drwx------+ 10 myuser staff 320 Aug 27 04:51 FontCollections
drwx------+ 19 myuser staff 608 Aug 23 22:06 Fonts
drwxr-xr-x 3 myuser staff 96 Aug 10 11:44 Dropbox
drwxr-xr-x 9 myuser staff 288 Aug 10 11:44 LaunchAgents
drwxr-xr-x 20 myuser staff 640 Jul 13 13:08 iTunes
drwxr-xr-x 18 myuser staff 576 Jul 10 16:18 LanguageModeling
drwxr-xr-x 2 myuser staff 64 Jul 7 16:46 QuickLook
drwx------ 5 myuser staff 160 Oct 25 2016 Personas
drwxr-xr-x 2 myuser staff 64 Oct 23 2016 PDF Services
drwxr-xr-x 3 myuser staff 96 Oct 23 2016 Speech
drwxr-xr-x 3 myuser staff 96 Oct 23 2016 Workflows
drwxr-xr-x 5 myuser staff 160 Oct 18 2016 KeyboardServices
drwxr-xr-x 3 myuser staff 96 Oct 18 2016 Maps
drwxr-xr-x 3 myuser staff 96 Oct 18 2016 CallServices
drwxr-xr-x 3 myuser staff 96 Oct 18 2016 Sharing
drwx------+ 3 myuser staff 96 Mar 22 2016 Internet Plug-Ins
drwxr-xr-x 6 myuser staff 192 Mar 13 2016 Address Book Plug-Ins
-rw-r--r-- 1 myuser staff 528 Jan 5 2016 ._bundleInfo
drwxr-xr-x 3 myuser staff 96 Dec 26 2015 Polyverse
drwxr-xr-x 3 myuser staff 96 Nov 23 2015 HipChat
drwx------ 3 myuser staff 96 Nov 15 2015 Saved Searches
drwxr-xr-x 5 myuser staff 160 Nov 2 2015 PubSub
drwxr-xr-x 3 myuser staff 96 Nov 2 2015 CoreData
-rw-r--r-- 1 myuser staff 0 Nov 1 2015 .localized
drwxr-xr-x 3 myuser staff 96 Jul 6 2015 A1AUDIO.de
drwxr-xr-x 3 myuser staff 96 Jun 6 2015 Frameworks
drwxr-xr-x 3 myuser staff 96 Jun 6 2015 Java
drwxr-xr-x 3 myuser staff 96 Jun 6 2015 Python
drwx------+ 8 myuser staff 256 Jan 14 2015 Audio
drwxr-xr-x 4 myuser staff 128 Jan 9 2015 Developer
drwx------ 5 myuser staff 160 Nov 7 2014 Social
drwx--x--x 2 myuser staff 64 Oct 30 2014 GameKit
drwxr-xr-x 3 myuser staff 96 Oct 29 2014 Twitter
drwxr-xr-x 3 myuser staff 96 Oct 29 2014 ColorSync
drwx------+ 2 myuser staff 64 Oct 29 2014 Assistants
drwx------+ 2 myuser staff 64 Oct 29 2014 ColorPickers
drwx------+ 2 myuser staff 64 Oct 29 2014 Colors
drwx------+ 3 myuser staff 96 Oct 29 2014 Compositions
drwx------+ 3 myuser staff 96 Oct 29 2014 Favorites
drwx------+ 3 myuser staff 96 Oct 29 2014 Input Methods
drwx------+ 2 myuser staff 64 Oct 29 2014 Keyboard Layouts
drwx------+ 2 myuser staff 64 Oct 29 2014 Screen Savers
drwx------+ 2 myuser staff 64 Oct 29 2014 Services
drwx------@ 2 myuser staff 64 Oct 29 2014 Sounds
drwx------+ 2 myuser staff 64 Oct 29 2014 Voices
drwx------+ 4 myuser staff 128 Oct 29 2014 iMovie
drwxr-xr-x 3 myuser staff 96 Oct 29 2014 Dictionaries