2.4GHz is supposedly immune to interference, but I was told that a couple of clubs in the UK have a problem with nearby telecomms masts swamping model signals.
If its losing signal, where is the RX aerial? Its pretty much line of sight, anything in the way that can block a signal, will.
Another possible is a bad power connector. The batteries might be in great condition, but there might be an uncertain connection on the way to the RX. If that loses power, effectively the signal is lost and everything has to restart.
During recovery, was the TX left switched on? Was it throttled back? What sort of ESC is fitted? Just curious because of the motor running when taken out of the water.