https://support.klei.com/hc/en-us/articles/360029880551-Oxygen-Not-Included-Troubleshooting-Guide

Problems caused by official guide (among others)

• Need to reinstall ALL mods, not only affected ones
  
• Loss of all config settings, including mods
  
• Loss of some save data (mainly autosave thumbnails. Save files tend to have Steam cloud backup, though this can backfire in other ways)

The steps provided will at least avoid the problems above, except you will still lose settings only for the mods you need to reinstall, but nothing of the others.


Throughout all steps, ONI should always be running (at least in the background) or being restarted as instructed.

1. Open ONI, bypass prompts with ESC.



2. Alt-tab to Steam, open the mod's workshop page, note down the mod's number from the url, then "Unsubscribe" the mod (Tip - click on the URL to copy to clipboard). Repeat for all other mods also coming up in the prompts.



3. Alt-tab back to ONI, once it reports mod(s) are uninstalled, restart ONI (even if not prompted - not sure this is critical to succeed, but it clears off the "Restart" notices and resets error reports in the Mods toggle menu).




4. Open

\Documents\Klei\OxygenNotIncluded\mods\Steam

in Explorer, identify the mod (folder with same number as mod), and "Permanently Delete" (skip recycle bin) that folder.

1. With ONI still running, pause/shutdown OneDrive
(do not allow OneDrive to resume/reactivate till the last step in part 3)




2. Access Onedrive via browser, open the Recycle Bin & delete the newly removed mod files/folders

1. With ONI still running & OneDrive paused/shutdown, open mod workshop page, re-subscribe to the removed mods.


2. Return to ONI, enable the mod, restart when prompted.

(if successful, this should be the last restart prompt you see)


3. Checklist before continuing (if not, you might want to redo from beginning of Part 1)

• OneDrive remains paused/shutdown since Part 2
  
• ONI is running

4. Now, reenable OneDrive, allow it to finish syncing, then close ONI only after OneDrive has nothing else to sync.



For best results, keep ONI open until the below is fully complete