Prior to recent phone dying, I had found out that Google's photo backup strangely (or at least sans a setting I was missing) MOVES files off your phone that they backup. Once I realised that I excluded all new folders created from this "backup". Of course when I get a phone replacement, and choose to recover the old phone's stuff, don't expect those to be there.
So that I don't end up in the same situation again with the next phone, with Google photos backup is there any way to retain a copy of everything backed up on the phone?