In addition to Bill and Scotts insight, BH can survive in moist mud for periods of time even without surface water - from what I've read. That's why I think allowing the pond to dry for a period of time would also be beneficial. If you want to renovate by adding depth, removing organic material/silt, ect the equipment would help ensure any surviving/hiding BH are removed. I'd go tabula rasa here in your shoes.
Due to the cheap cost of hydrated lime and stubborn nature of BH, I'd second Scott's vote and perform a second application. FYI my cost for hydrated lime was $9/50# bag.