Sorry to hear about the lily pads!
My father once had some extra fertilizer left over, so he did our backyard at double the recommended rate. It burned the hell out of the yard. That taught me that "If a little is good, more must be better!" is not always a true statement.
I didn't think a little fertilizer would be bad for your pond. However, a LOT of fertilizer might be bad for some of the plants? (I have no clue which aquatic plants are most likely to suffer if there is excess fertilizer in the system.)
We do have some actual lily pad experts in the forum. Post a couple of good pics, and maybe they can help save them.