I'm actually doing the WC in the show tank that is connected to the breeding tank, so the new water doesn't go directly into it. Not sure if that helps.
I wonder if moving the fry into the show tank would make any difference, after all it's the same water. I'm confident they would be able to find their parents, but perhaps not the BBS that could get lost in the gravel. Not that they go for the BBS fallen to the bare bottom either.
Honestly I believe this is where your problem could be.
most breeders would not share water from an established tank but keep the breeders in a more isolated tank where you can control the parameters easier and control the incoming water.
the fact that the breeder is sharing water with your display tank could be contributing to the issue.
the young discus don't have much in the way of protecting themselves as they have not developed their immune system so they would be very susceptible to bacterial issues.
it is one of the major problems when having breeders. I have successfully bred Angels by using isolated tanks for the fry, they are (in my case) removed from the parents at the free swimming stage and place in a controlled growout tank that gets at minimum 50% daily water changes.
you would need to try this to see if this helps, I have rarely seen discus raised in any other way but have actually raised angels from egg to dime sized in the parents tank.(most often I find the parents eat the young tho). even those are controlled isolated systems that do not share water for systems.
