So I finally figured out that I had to delete my workspace and create a new one.
But I wanted to keep all of my formatting of the colors and font styles that I use in the Flash builder editing space so I used the following:
I ended up using the method of copying the files from the .settings folder over, worked like a charm.
1. Close Flash Builder
2. Go to the the following folder: ( replace USERNAME with yours, path, etc... )
**C:\Users\USERNAME\Adobe Flash Builder 4.7.metadata.plugins\com.adobe.flexide.codemodel.bridge\searchCache **
3. Delete all the files contained in this folder.
4. Restart Flash Builder
5. Clean all your projects. Go to Project->Clean->Select Clean All Projects.
See if that works for you