There are many variables here which make deciphering the event very challenging.
Once the flood waters subside there would have been land locked fishes which would have certainly perished during evaporation; leaving fossils. There is also a possibility that surviving birds could have fed on these fishes transporting the carcasses to other locations; removing fossils. In addition flooding on the scale described would also cause enormous erosion, transportation, and deposition events which would really mess up any theory of a well-sorted fossil record.
The flood certainly could have taken place and in most likelihood was the result of a glacial dam break, or series of breaks, that could have occurred many hundreds of miles away. Since the perceived size of the world back then was in reality quite small this recorded event may have been much smaller than the biblical account indicates.
I think there was a global event on a scale not seen in a long time.. Many civilizations speak of a major event similar to the flood.