I think the exception happens here:
Duplicati current calls something like
https://apis.live.net/v5/<folder>/files to get the list of files. According to this document, there are a few new ways to call it:
It is possible that they somehow broke the old API. In that case we would have to re-write the OneDrive backend.
For the duplicate files, is there any sense to it? It appears that it just shows random sizes. One very ugly hack, would be to only pick the largest file. This should work, as Duplicati does not overwrite/append/modify files, so the largest file would be the latest.
That idea would hide any flaws that the OneDrive API has, which could lead to more headaches later on, or just work perfectly