I just bought an Marlin 7000 and the manual says no hypervelocity ammo. I was thinking of shooting Velocitor ammo before I read this statement. Has anyone been shooting these types bullets in this rifle? Is there anything I can do to prevent harming the rifle if I shoot the hyper ammo?

At a guess, it may be a legal thing to keep them from being sued, kind of like "Never use reloaded ammunition..." in every gun manual I've read. To be sure, you may want to contact Marlin.

The only round you shouldn't shoot in match-grade barrels (if it's a match barrel) is CCI Stingers; the case is longer and they usually won't chamber. But I don't know if that's the issue with your Marlin.