Agreed Maggie but water quality may well still be an issue whilst the OP still uses dip test kits as we both know they arent that accurate at the best of times .@Dave 54 I didn't get the impression that the OP was necessarily trying to breed the fish (Shubunkins, from the sound of it) but that they "just happened," and now some of those fry are dying off, etc. and he's wondering why...... I think some of those possible reasons have been covered (normal attrition, canibalism, pond predators......to name a few).
He has had fry before, but [apparently] has never has a die-off like this before. I can't help but wonder about the problems he was having with the pond back a month or so ago, and wonder if that has anything to do with this? I think there was some question as to whether a chemical agent accidently got into the pond and was killing the mature fish vs. general water quality issues [over-crowding]. Even though he's cleaned the pond, what if there were chemicals present initially.... Would they have all been removed by a cleaning? Would filter media be harder to clean from that standpoint? And what about the chemical effects on the parents possibly causing "genetic" type issues? Not saying this is what's going on [I thinks it's normal attrition, etc.], but you do have to keep the HISTORY of this pond in mind.
It may well be chemicals still but who really knows not until we get the whole picture and perameter readings from a reliable drop test kit .
The OP knows how well the pond was cleaned if the OP says it was well cleaned as was the filter then I cant see that being a problem can you ?
Dave