QSYS throws error when generating DDR2 UniPHY RAM

Since you say you've previously successfully generated this system, I'd try trashing the directory that was previously generated (named after your .qsys file). That directory is usually overwritten when you regenerate a system, but it can't hurt to try.

Other than that, have you made any other changes to anything, like move the project files to a different location or anything else?

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