i would stop treating them until they are larger and hardier, fry for bowfin are pretty touchy sometimes when it comes to stuff like that even though I have caught some larger ones in pretty gnarly places that the water conditions were not so great in
i would just keep doing regular water changes and have a sponge filter on the tank until they get around 3-4" long before i would start the treatments again but if they make it to that point then i would bet they are going to be fine