I tried to do some troubleshooting on my own, but the SDK and selection of .flt files is nebulous enough that one doesn't stand out at me. There's finalwater.flt, that doesn't seem like it, runwaywater.flt, which is the only other water one I suppose. Why is there no apronwater if you can spawn on the water C&D?
I tried loading in with all of the .flt files removed from the directory in the hopes that I could force the sim to generate one (or save my own per the SDK); I never figured out how to save the .flt file while loaded into the plane to see which it spits out. Doing the above procedure without any .flt files present in the directory does mitigate the engine damage to a single percent, though, if that tells you anything.