My understanding at least with Mollies is that a transitioned female is not always fertile either. So yeah I would take it out and get a pair if you are interested primarily in breeding.

I also thought that in ciclids the parents will eat the babies at some point after guarding them for a while. But then I was reading the fish keeper magazines a LONG time ago so I am kind of just repeating vague memories....Are the ones that were separated ok?