General Description: When a Foundation Express project is restored (from an archive), all HDL files appear un-analyzed (each has a red ?). To re-analyze these files, select Synthsis -> Analyze All HDL Source Files.
If the project has been restored to a different directory path than the one used when the project was created, all VHDL files located within user libraries will not be analyzed; they will still have a red ? associated with them. This is due to the fact that FPGA Express uses absolute file locations. The VHDL files have been moved, but Foundation cannot tell Express where the files have been moved to.
Solution
Remove and re-add any VHDL files located within user libraries.