I think this should not be attributed to malice, however unfortunate. I had also developed some sync app once and onedrive folders were indeed problematic, causing cyclic updates on access and random metadata changes for no explicit reason.
Complete lack of communication (outside of release notes, which nobody really reads, as the article too states) is incompetence and indeed worrying.
Just show a red status bar that says "these folders will not be backed up anymore", why not?
What’s worse, random metadata change or a completely missing data?
If the constant meta changes (or other peculiarities involving those folders) make the sync unusable, then it can be both. In that case, you stop syncing and communicate.
So my idea is that it's a competency problem (lack of communication), not malice. But it's just a theory, based on my own experience.
In any case, this is a bad situation, however you look at it.