I've heard of re-coating rubber roofs with a paint-on rubber compound. One of our members, Dave Derway, has done it and I've heard of others elsewhere. It appears to work OK and it's a whole lot cheaper. Difficult to get it looking as nice as a replacement, though. On the other hand, the roof isn't very often seen either - just the edges.
I see no reason a new rubber material could not be layed over the old one AS LONG AS THE ORIGINAL IS FIRMLY BONDED to the roof structure. But if the reason for replacing the roof is bubbles (the original rubber roof has become unglued), then it's got to come off first.