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Before you go trashing your save file, my game has started crashing when I access the private storage, every single time. I was using mods too, but I also backup my saves using Ludusavi to my NAS, as a quick test I restored my save file back to way before I installed the first mod and it still crashes.
My entire game has been unstable since updating to 1.0.3.
I'm assuming you have backed up your saves with Steam Cloud? You can check you cloud data here: https://store.steampowered.com/account/remotestorage
Step 1
Firstly (assuming you are on Windows) backup your saves from here
Step 2
Uninstall the game through Steam, then delete all mods and symlinks through whatever mod manager you are using.
Go to your games install directory and manually delete the folder as any mods will have left remnants here.
Step 3
Reinstall the game and try playing it, hopefully your cloud saves will be restored and everything will be swell. If so, happy hunting, if not continue.
Step 4
Disconnect from the internet, make another backup of your save directory (Step 1), then delete those saves and restore your manually backed up saves. Now, a bit of trial and error. Try loading older saves, I went a step further and deleted the actual save files from the SaveGame\Data directory. If a mod has corrupted a save, it will have only corrupted the save files from the time of install onwards.
IMPORTANT While fiddling with your saves stay disconnected from the internet otherwise you will force an upload and clear the data in Steam Cloud. Only reconnect once you are happy it is working.
With any luck you will only lose an hour or so of effort. Fingers crossed for you.
On a side note, I would strongly recommend everybody uses a tool such as the one below. Ludusavi is open source and cross-platform, it can be configured to back-up all your saves to a directory with a configurable number of full back-ups and differential back-ups. This is specifically the tool that allowed me to easily recover my saves.
Edit: forgot to link Ludusavi
https://github.com/mtkennerly/ludusavi
Also I don’t want to redownload the entire game again, because my internet is really slow it will take a few hours and the internet provider I have has a cap on how much I can use per month.
I get you, the alternative is that you are going to have to scan through all the files and manually check that none of them are modded. (pak, config etcs). If the files are changed by a mod rather than adding new files, then a reinstall is the only way.
As a first test, just delete all the mods, manually check that all the mods have been deleted in the game folder too. Then run from Step 4 onwards. You might get lucky, it all depends on what the mods changed. Sometimes they just add paks, sometimes they edit game files
Did you have any luck restoring your saves?
Have you tried uninstalling fully, and manually cleaning up the directories before installing again?
Do I need to remove other files after removing 〜mods
it entirely depends on the mods you had installed. If they directly altered game files rather than being self-contained paks (or what have you) then you will need to restore the originals. But theoretically yes, in an ideal world that would be the end of it because the mods should be liked via a symlink so none of the original game gets changed, I don't think I've ever seen it work out that cleanly when you have a few mods installed.
With that said, as I mentioned to OP, if bandwidth is a problem, start with the easiest and least destructive steps first. So yeah, delete the ~mods folder and load an older save file, If that doesn't work have a scan outside of the ~mods folder.
Honestly, if you have the bandwidth to do a full reinstall this is the easiest way to recover from a corruption. The Steam "Verify Installation" has never fixed a broken game for me, it always leaves the modded files behind.
If yes, then update 1.03 most likely broke your save game. The modded items just broke the inventory and are causing CTDs. We should have updated the mod before loading the updated game. Even if you uninstall the mod, the inventory will still crash. you basically have to find a save game before you installed the mod and play again OR you wait for a future update where, hopefully, the game automatically deletes missing items from the inventory.
A lot of players have this problem, including me, and you may find more information on the nexus side of mutant loot.