The problem is that they probably won't chamber in your gun, because it disrupts the head spacing. And you certainly don't want the slide slamming down on the primer (which is the highest part) and setting it off. That's the whole point of having them below flush.
What you can do is run them back though the press at the primer seating station. It's not optimal, but it can be done. I want you to slip it in station #2, then (with your safety glasses on) you can stand on the opposite side of the press structure so that you can't see the cartridge, then apply very slow, steady pressure to fully seat the primer.
It will be OK.