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 `