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I'm wondering how you would be able to compile your project (hence why you would open your project) if you don't have access to the files?
If nothing else, I recommend using a version control system like Subversion (Subclipse plugin for Eclipse is GREAT) to manage files that might disappear when you aren't on the network. Set up a repository, then update/commit the files when you're on the network, and you'll have them up-to-date when you're offline. The added bonus is that you have version control.
I guess i wasn't that clear. If my network share isn't available while FB2 is running then the files in the project folders are no longer avail (obviously).
What is puzzling however, is when the network share is up, FB2 will no longer retrieve them. In order to get the contents of the project, i have to re-create the project.
This is happening on both Windows and Mac.
Because this seems to be an issue with Eclipse, and the lack of official comments on this, you may get a better response at the Eclipse website...
Might as well try both!