Hi farmchef,
Sorry for the late reply.
Thanks for your update.
If the conditions permit, could you please use ediscovery to search the items which are in the missing folders.
You can refer to the link below.
blogs.technet.com/.../single-item-recovery-in-new-o365.aspx
Moreover, could you please contact the other two users to confirm whether they have done some actions?
Thanks for your time and efforts.
Regards,
Jerry