Saved Sims missing in CAS but are still in SavedSims folder

@AgentDolphin  Uninstalling the game entirely is a last resort, and I doubt it would help you in this case.  Your problem sounds like it originates in your TS3 game folder in Documents, not in the Program Files.  The game folder is much more easily manipulated and regenerated if necessary, as you've found out already.

There may be a simple solution to this, but as I don't use custom skins (or really, any cc at all), I wouldn't know how to address this specific problem.  I can tell you how to try to fix your game folder in general.  However, for cc help specifically, it's better to ask on one of the hosting sites like MTS.  Many of them have forums to provide support to users.

Did you delete any other files in addition to the one you mentioned?  In cleaning up your game folder, you might have inadvertently trashed some other file related to your custom skins.  Also, if you saved after you saw the problem in-game, replacing the one file wouldn't necessarily undo the damage.  In that case, it would be better to revert to a prior save; if you don't have one, you can rename the .backup save to something else (and remove the .backup from its name), and it will then be available for you to load at the Main Menu.  If this is not an option, you can re-add those skins to the sims that need them, assuming you can get the skins to appear in CAS again.  Even without mods, you can edit in-game sims in CAS: enter "testingcheatsenabled true" without quotes in the cheat console (crtl-shift-c to bring it up), and then shift-click on a sim to see the option.

If you can't make your saved sims or their cc show up in-game, the more drastic approach is to rebuild your content in a new game folder.  Move your existing folder out of Documents and onto your desktop, and a clean one will spawn the next time you launch the game.  Copy the contents of your DCCache and SavedSims folders into the new TS3 folder, along with your Mods folder if you have any skin-related cc in .package files.  Then copy over one of your saves and load it.

Is there still a problem?  You might be stuck reinstalling all of your content in your game folder.  But if you still have the .sims3pack files associated with those original sims, you can try uninstalling and then reinstalling only those files through the launcher.

If none of this helps, it's probably best to ask at a dedicated cc site.  But again, you don't have to go through all the trouble of uninstalling and reinstalling the entire game.  At most, you'll need to rebuild your game folder, which is still a pain but better than messing with program files and the registry.  And once you're satisfied with how your game folder is functioning, you can move over your existing saves and fix any sims that aren't showing the proper skin.