Downward compatibility in Quartus

New features often have .qsf assignments that are added in that build to show what it's set to. When you go back to an old version, it has no idea what those .qsf assignments are(as far as it knows, you completely made it up). There's no way to go back and patch the old software to be aware of this. And the reason it errors out is to catch problems if the users are manually editing their .qsf(i.e. error out that the assignment makes no sense, rather than continue on and ignore it).

Anyway, most likely these .qsf assignments make no sense to 6.1 and are irrelevant. Either delete them or comment them out. (If you delete them, and then migrate the project back to a newer version, Quartus will add them back in, like it did the first time.)