Whatever happened, it is really important to keep the
nitrate, ammonia, and
nitrite as low as possible.
If the fish are developing bald patches, my first guess would be either a bacterial or fungal infection.
How you treat this may be affected by how many fish seem to currently be infected. If there are only a few, you may want to set up a quarantine "tank" made out of a wading pool. You could treat the pool with a broad-spectrum treatment (look for something that treats both bacterial and fungal).
You could also treat the pond with Melafix. This will likely help protect the rest of the fish from developing a full-blown infection.
If a lot of the fish are infected, it's probably best to just treat the entire pond (if you can get a bunch of filter media and put it in a Ziplock bag in the fridge, that could help you restart the cycle when you're done treating).