The error you receive is expected as per documentation from Mendix (see below).
Similar information was posted here on how to clear repo: https://forum.mendix.com/link/questions/10222
But it seems that this did not work, maybe because they did not clear it fully.
What you could try to do is to clear the entire repository by deleting everything and committing from the SVN context menu from the file explorer. Then try to upload your project to this repository.
I’d do this in a test application first to see if it works without corrupting anything.