Are the project files physically deleted, or you just can't see the project -- not sure by your question. If not deleted, but you can't see it when you do a MODIFY PROJECT ... command, try:

_VFP.ActiveProject.visible = .T.

You should also be able to select the project from the 'Window' pull-down menu. If after this, you can see the project, then somewhere you are setting this property to false.