I always overwrite a save, and never have experienced any adverse behavior. I have also saved while submerged, a known "no no", but again, mabey due too luck, nothing adverse. The only thing I do really try to watch is the time of the save. There is an issue as to the in-game save hour, and problems with your whole crew turning in for a good nights sleep, all at the same time. Not a good thing
Other than that, I can't really say I've had any issues with overwriting game saves
