I used One drive For Business (ie 365) for a small number of files in a small number of folders. I later installed OneDrive Personal (to assist a niece who had issues and could only use OneDrive Personal to see the files she wanted to share with me). Very soon afterwards I found all sorts of anomalies.... I discovered shortly after that Windows had moved my Desktop onto OneDrive (Personal) plus lots of Desktop sub folders, plus lots of other Library Folders, such as Pictures, Music, etc. I was unaware that Microsoft/OneDrive would make such drastic changes to my PC config. I specifically did not want these folders in the cloud. Because I was configuring a new laptop at the same time, these changes rippled thru to other PCs I own. It took me months to unravel the mess, I am still not sure if I have got back to where I started.
My philosophy with disk storage services (such as One Drive, DropBox, iCloud, etc) is that any files or folders I copy to these services are purely for the convenience of replicating the files on another PC (and I never use these services for backup purposes) and that I am prepared to lose these files or folders at any stage (because I keep the originals in my original folder structures outside of the virtual storage services).
I am not suggesting that everyone follow my methodology on this..... but there may be some aspects of the behaviour of OneDrive on your installation which may be causing you these issues. For example, the root cause may stem from file admin taking place on a different PC of yours which may overlap the OneDrive installation on that remote PC.
Of course, this may be irrelevant to your scenario... but just wanted to flag it as a possibility.