Haven't made a team-switching spawnroom in any of my own maps, but if I recall correctly here's what you need to do--
You need to double-up your spawnroom entities, so that RED has a set and BLU has a set. One set should always be disabled. When it's time to switch which team owns the spawnroom, disabled RED's spawnroom logic and enable BLU's.
I think some entities might be able to have their ownership directly changed, but I can't open up Hammer right now to verify. I know for a fact that spawn points can't.