So I haven't completely thought through this, so don't just go ahead and do it. Definitely test first. Also if anyone sees something terribly wrong don't be afraid to say.
Seeing as you're only using SimpleStrategy and it doesn't care about racks, you could change to SimpleSnitch, or GossipingPropertyFileSnitch with just 1 rack, by changing snitch/rack details and setting -Dcassandra.ignore_rack=true Do this for all nodes until you have 40 nodes in 1 rack, then change to NTS with RF=3. Then do a DC migration to a new DC with the correct configuration of racks (ideally >=3 racks). Unfortunately DC migration is currently the only way to change RF and rack topology without downtime.