I would be more concerned with the treatment harming the fry after they are swimmers. I've routinely added antibacterials & antifungals to a variety of species I'm hatching out at a concentration greater than what would normally be used for free swimming fish. Once they are swimmers you want that concentration to be half or less of the normal dosage.
I've had bristlenose kick the eggs out of the cave on occasion for whatever reason, often doing what you are doing using a 2.5 gallon tank. They hatch, get fed for a few days, and get put into a larger growout tank, no different from those hatched by the male.