This is often a problem with temporary files saved by eclipse plugins.
Check YOUR_WORKSPACE/.metadata/.plugins/org.eclipse.jdt.core/.
There are a lot of index files. Sometimes it helps to delete them.
Also, start your eclipse with -clean.
But I think your problem is slightly different.
Did you have a reference to a library(jar-file) somewhere in your filesystem?
If you deleted it or moved it, eclipse can’t build your projects.
Did you refresh all your projects?