Amazingly, I can report, that my issue resolved itself without any further action from my side. Whether this was helped by an e-mail I sent to Microsoft support a few days ago, I don't know, but most of my OneDrive is back to normal, just 45 days after Microsoft screwed it up. Solely my secondary computer, which holds a few files and directories as local copies too, replicated these to the cloud during the issue period and now failed to remove them completely. I was left with a mirrored directory structure containing no files. Deleting those empty directories manually seems to have resolved the issue though.
I wish you all the same luck with your OneDrives in the very near future!