This seems to be partly/mostly a Photoshop problem, but here goes anyway:
I have an image that I opened in Photoshop and launched ReMask from there. Did my masking, had ReMask create a layer mask for me. Later I wanted to remove an additional part of the image so I duplicated my layer, applied the existing mask, and ran ReMask on it again. When it opened in ReMask, all of the original image (the part that had been masked out) was still there. I tried several other things, including, finally saving the file to PNG and reopening it in Photoshop. Same result: in Photoshop, the content that has been masked out is not visible (and it correctly shows that there is currently no mask for the layer), but when I launch ReMask (from Photoshop), the content is still there.
So apparently Photoshop retains the original layer content even after the mask is applied (does everyone already know this except me?!), and however it gets passed to ReMask, ReMask is showing it.
When I open the PNG file directly in ReMask, instead of launching from Photoshop, things work as expected.