So, this is my first post and I will try to be as detailed as possible.

I have this save I've been working on for over a month. I've been very careful to use "Save As" and then quitting, as opposed to "Save and Quit" because I heard that leads to corruption easier. Every single time before I boot up my game, I clear my cache files/tidy up my S3 folder but I'm careful to not delete files I'm not supposed to. (Although after writing this post, I'm wondering if I accidentally deleted something I wasn't supposed to?)
I do have NRAAS mods installed (Traveler, Story Progression, Decensor, Error Trap, Master Controller, and Overwatch) and I have a large mixture of .sims3packages and .package files as far as CC goes. I play with all my purchased EPs, SPs, store content, CC, and mods ENABLED at all times.

Now last night, my game was perfectly fine. I played for about an hour and a half and then I "Saved As" for the night. I go to start my game today and when my save loads, it gives me a notification that objects are missing but they've been replaced. I find that odd, so I double-check my expansion packs are all enabled (as I'm sure you know the Launcher can be funny sometimes) and they already were. So I started my game again only to get the same notification. This time, however, I notice one of my Sims' CC hair has been replaced with base game hair. Worried, I opened CAS up just to scroll through my CC hairs real quick and I notice quickly that a majority of them are missing, BUT a choice one or two still show up. She was still wearing her CC pajamas, so I figure the clothes and shoes are having the same problem.

I exit the game and look at my Sims 3 folder. All of my .package CC is still in its proper place and theoretically should all be installed.
I look at the Launcher to look at my Installed Content and find that most, if not all, of my .sims3packages and store content files are completely gone. I had a SERIOUS list of CC and store content on this list.

I'm troubled because everything was working perfectly fine last night and now it's not. I'm particularly attached to this save and I would be heartbroken if I had to uninstall the game and start all over. I tried looking at other threads in this forum but none that I saw described my problem close enough. I would be very grateful if someone could point me in the right direction of fixing this. I'm not particularly tech-savvy, but I'm pretty friendly with TS3 folder, so I will do my best to follow along!

Installing and uninstalling the game involve the game's program files. Your added content is not a part of that so doing so wouldn't really accomplish anything.

In the TS3 user game folder in Documents that you are working with, your already installed sims3pack content would be in bundles in the folder called DCCache. The ebc bundles are TS3 store content, the dbc bundles are CC. Any tmp files in there are expendable garbage. Since it is CC you have identified as going missing, do you see dbc files in DCCache and are they numbered sequentially, with no numbers missing in between and starting from 0 like this?
dcdb0.dbc
dcdb1.dbc
dcdb2.dbc
etc.