I think this is the issue. Somehow when there are two PCs, both syncing, OneDrive gets 'confused' and starts deleting all the files that appear in conflict, when it should simply be XOR'ing the files and updating to the latest draft. Somehow, despite the same directories and files being on the two PCs, the comparison is finding that the directories on one are somehow different and 'older' than the other, and deleting data without simultaneously copying the newest data to the local store.
It may also be a versioning issue; I run OneDrive on a Mac and a PC, and the deletions seem to happen when after I access the cloud share from a different PC, in my case, the Mac.
I haven't had any response or inquiries from Microsoft regarding this problem.