I have an Eclipse project (Flex Builder) of which the actual files have changed location on the drive. When I start Eclipse I can see the project listed but there are no act
Using Neon - just happened to me too. You would have to delete the Eclipse version (not from disk) in your Project Explorer and import the projects as existing projects. Of course, ensure that the project folders as a whole were moved and that the Eclipse meta files are still there as mentioned by @koenpeters.
Refactor does not handle this.