Here are a few places to look:
1) Window | Preferences, then Gneeral | Workspace, the check boxes at the top
2) In the project's properties, look under Builders -
you should have a
Java Build entry that is checked.
3) Are the directories containing your Java source files still marked as source directories?
I'm sure that there are other things that can go wrong, but these are the ones I can think of off-hand.