It's just overlap. Once you update all of them to the new URL, those errors will go away.
It'll be much clearer what's going on if you temporarily name the repositories different things. Basically the new repository is saying "I own these add-ons: A, B, C", but add-ons A, B, and C specify in their version.txt file that they're owned by the old repository. The same happens in reverse: the old repository claims to own Brick_Doors_Frameless, but Brick_Doors_Frameless specifies the new repository in its version.txt file.
The error is harmless so long as you control both repositories. The purpose of it is to prevent people from taking over others' add-ons using their own repository.
Also, I see that you got the PHP script set up. Very nice.