Some sites use deformation in cases where the shape is restored by elasticity - in that case the energy comes back as kinetic energy as the shape of the ball rebounds, pushing it away from the surface.
This one, for instance does not count deformation as "energy lost"
A very nice previous answer describes some of the effects of squash
ball
deformation and elasticity:
It does mention "internal friction" (ends up as heat), heating, sound (ends up as heat) and vibration of the ball (most or all of which is likely to end up as heat).
In other sites they talk about energy breaking molecular bonds - in the case of water this would be the weak hydrogen bonds between molecules. I'm not certain how that works out, but in a "Flood" situation new bonds will be formed anyway - so I expect that the net effect will be zero.