Seems I am your most frequent visitor to this thread
I have two Kobos, a Mini and an Aura.
I managed to get both the finished and reading shelves on both readers.
While doing this with the mini I selected all books with a reading status and used the restore bookmark function. I have quite a few books accidentally opened on both readers and maybe a dozen or so in progress books.
I looked at the Reading shelf on the Mini and had 47 books which seemed excessive. Then I noticed that some had an unread status and thought they had been reset, but remembered that I was actually reading them on the Aura.
I can avoid this happening again by filtering by ondevice , but thought it might provide a way for those who want to sync between Kobo readers with sideloaded books to do it.
Helen