I would suggest destroying all contents of destroyed factory and killing player (if inside).

Right now - during my testing I was able to do this :
place factory (it takes slot 1)
go in, place factory (it takes slot 2)
go out, spawn some biters in editor mode. They start hitting factory1. Go into factory 1. Wait for biters to destroy it (you don't die, you are still in factory 1 that was destroyed). Go into factory 2. Place 3rd factory and it will take slot 1. From now on - moving out of factory 2 will teleport you to factory 3 and moving out of factory 3 teleports you to factory 2.