Good question. It may also have happened when testing remastersys, but mostly I used your software as I find it makes more sense to exclude what isn't needed rather that decide what to include(Remastersys). If I have a fully working setup, I know if I include everything it will work, so like I said, it just makes sense to me to exclude things that are not needed. I have made some lovely remasters using both remastering softwares.
I have had the very same issue with XDG occur with Debian Xfce.
I once wrote to the XDG developers but found no answers. I know the file, /user-dirs.dirs in /.config gets recreated during login. I had found others online with the same issue, who suggested deleting the file and logging out and back in, and sure enough it puts everything back to normal.
The remastered live DVD starts up with everything in it's proper place. It is just the installed system this happens to. As I mentioned, I am not 100% sure it is the remastering process that causes this bug, but it has happened very often to setup's that I had created remasters with. Very strange indeed.
The first time this happened, I made the mistake of thinking the folders that appeared all over my desktop, were just linked or copied, and I deleted them. Must have needed sleep. I deleted all my data