Using Classic Outlook on Windows for personal email, calendar, and contact management
Here's something that might work for you. On the computer where they still are marked unread (I assume you're looking in Outlook desktop's Unread Mail search folder), select them all. When the sync completes and they are all marked as read, they should still all be selected. At this point, you should be able mark them all as unread again which, in turn, should propagate back to the other machine.