From: timjowers on
I figured this might help some other java programmer. Eclipse likes to
give this error when working with multiple projects and you try to
import another existing project: "Some projects were hidden because
they exist in the workspace directory"

The fix is to edit the .project file in the projects directory. Change
the name:
<name>FlexWebApp</name> in the project description.

This occurs when you have default names given in Flex Builder or
others and you do not change these.