I've run and re-run to tool on steam to verify the integrity of the game cache, and 1 file always fails to validate. I've been getting lots of CTDs and I'm starting to think it's this 1 file (I have no idea what this 1 file is and I never actually see a file download on steam after it says it will be reacquired). Am I doomed to do a full reinstall? Sadly I use a few stat/perk related mods, and I'm wondering if I have to reinstall everything will my save keep track of all the non-vanilla perks I've chosen or not from mods, or if I'll have to restart any mod quest-lines. This is the first time this sort of thing has been a serious issue that I haven't been able to fix with a simple update of all my mods and a quick use of BOSS. I'm assuming my load order is good, since I keep boss up to date. Any help would be appreciated.

Look at gamevalidation.log in the main steam directory. Open it in notepad.
What file does it list? It's probably installscript.vdf. If it is don't worry about it. It's a common issue that this lone file fails to validate. Does on my copy too.

What mods do you use? Could be a mod issue. Did it just start all of a sudden?

Backup this folder: C:\Users\\Documents\My Games\FalloutNV\Saves

Mod troubleshooting:
Load your save then make a NEW manual save. Exit the game and uncheck all your mods and disable archive invalidated. Load the manual save but DONT overwrite it. You will be prompted that some content will not be available. Just continue. It's because you disabled your mods. You are free to make a NEW manual save and quicksaves again don't overwrite the save you loaded since that is the modded save. From here just try the game for awhile and see if it is more stable. Look 4 CTD's. If it seems stable then you'll have to recheck mods and try again.

Alright, I'll try all that. The file listed in the log is the one you mentioned, scratch that one I suppose. So just to clarify, as long as I have a save set away WITH the mods enabled, if I end up needing to reinstall the game, mods included, I should be able to re-use that save and mod progress will be saved?

Correct.