Moved assets out of Resources folder: the namespace already contains a definition

I had my entire project in the resources folder. I moved it all out and now I get a bunch of error cs0101: The namespace x already contains a definition for y errors in dozens of scripts, my own scripts as well as scripts that come with unity (such as image effects).

I tried closing and reopening the project without saving so I can at least make a backup before trying again. But unfortunately unity likes to save certain changes without my permission at random.

Please help. :(

UPDATE: I right clicked the whole project and selected reimport all. After it was done it revealed a duplication of my project folder. I deleted the duplicate and some things were fixed and referencing things fine, but then some variables (at seemingly random) now have missing references. The projects pretty big, how do I fix this?