You are totally right! I ran some tests, and for every app I used to edit a given photo, one new file was created (even though we are able to see only as one single file). And then that causes the iXpand App to get confused.
I transfered non edited photos from my iphone to the flash drive with no problem. Those ones edited in Photos or Snapseed had that overwriting problem.
thanks for your help drlucky!!