I think you can find the answer you want in these two posts. They are mentioning Flash Builder, but essentially, the talk is about its Eclipse base.
Clear improperly cached compile errors in FlexBuilder: http://blog.aherrman.com/2010/05/clear-improperly-cached-compile-errors.html
How to fix Flash Builder broken workspace: http://va.lent.in/how-to-fix-flash-builder-broken-workspace/