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.
I will be doing it this summer. From all I can glean, the hard parts are mixing the compound and catalyst (the suggestion was made to rent a 3/4" heavy duty drill and paint mixing attachment), and working fast enough to prevent premature setup and curing. Keeping the mixture around 55-60 deg.F (maybe in a large washtub with ice water) might do the trick. I'll also do the trim and around vents, etc. first with a brush (masking first), then follow up on the major areas with a paint roller.