If you are using the Arduino eclipse plugin from eclipse.baeyens.it you may have noticed that your project got corrupted when you deleted a library.
I have debugged this problem and found this is a CDT problem which is out of my control. I raised a bug on CDT.
You can vote for the bug at 372807 – Deleting a folder corrupts the "Path and symbols"
voting for the bug increases the chance it will be fixed.
You will need a bugzillla account to vote.