As Princess Shmoo notes, the policy is that the two rooms need to be on the same cruise. In practice, if the two reservations are moved to two different cruises by you (via online changes), or by a
travel agent, you will (probably) keep the OBB on both bookings, or at least that's the way it has worked in practice for years. I don't know what would happen if you called and had a Disney agent move it; they might remove the OBB from one or the other, but I'm pretty sure it would be a manual action. They'd have to notice that you were moving one of a pair of OBB rooms, then would I guess ask you which one should keep the discount.
Obviously if Disney cared enough about this, they might figure out a way to make reality match the policy, so if you do do it, prepare for the possibility that one or the other cruise loses the benefits. But I suspect it would be hard for Disney to fix this via any automatic system. Right now, when you move two rooms, you just move them individually and then make sure the cross-links are still there (or re-apply them). If moving one room caused the OBB discount to get lost, it would get lost every time you moved a pair of linked bookings, because there's no "move two rooms at once" feature.
To be honest, I can't fathom why Disney would care. They put this program in place to get people to book more cruises in advance. Why would they care if you buy two rooms on one cruise or one room on two cruises? No other cruise line that I know of has a limit like this with their onboard booking program. A limit on number of total rooms, yes. But they don't care whether your rooms are on one cruise or several.