Error current license file does not support incremental compilation

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A funny thing is that Altera says they don't recommend editing the qsf file, but your suggestion to edit it is exactly what fixed my issue.

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It's fine to edit the .qsf file when the Quartus project is closed. Just be aware that you do so at your own risk (for example, you might create an invalid setting that you would be prevented from making through the GUI). Quartus will move certain kinds of assignments to the bottom of the file, so user-entered full-line comments might not stay with their associated assignment lines.