First, make sure your project is fully backed up or even better, put it under source control NOW in case something is going horribly wrong with it.
When properly using source control you should NOT be committing anything from the Library directory (see how to set up a .gitignore file).
Once you have it under source control AND TESTED in another directory, see if using it in that other directory works better.
If so, you should probably delete the Library folder in the original project, or perhaps Reimport All.
DO NOT TRY ANYTHING SUGGESTED until you have it backed up or under proper source control.
Source control notes:
Personally I use git because it is free and there are tons of tutorials out there to help you set it up.
As far as configuring Unity to play nice with git, keep this in mind:
Here’s how I use git in one of my games, Jetpack Kurt:
Using fine-grained source control as you work to refine your engineering:
Share/Sharing source code between projects:
Setting up the right .gitignore file:
Generally setting Unity up (includes above .gitignore concepts):