Yes. I completed Tyrannia 3, then cleared them all, earned and converted 1, 2, and 3 again, and cleared them all a second time. It works fine.
After that, I had an extra Tyrannia 3 lying around, so I converted it (without earning/converting 1 or 2 again -- it will let you do that for some reason). Now it won't let me clear them all again until I earn 1 and 2, though.