Well I managed to kill all the babies. Actually the parents killed all the babies technically but it was my fault.
I re-homed all of the other fish in the tank and in the process of netting them I had to take most of the rocks out and replace them after. I didn't think about it at the time but I ended up accidentally moving around the "home" shells for the babies. This freaked the parents out and caused them to have to find all new territory, which meant they disowned the kids and ended up eating them all not realizing they where there's.
This is all my theory of course but it makes sense. Oh well... They are still paired and hopefully will breed again soon! This time they will have the tank all to themselves lol.
"At some point you aren't making the animal more dead...You are just making a bigger mess." - Demjor19