Are the file name EXACTLY the same between devices?
Did ALL the books get ON TO the devices via Calibre?
In Calibre, switch to 'device view' (device is connected): For each book that is NOT ticked, right click Match to Library <you select the entry in the Library>
This procedure does not solve the 'sync' device issue. That relies on Kobo servers doing the match (I don't know what that needs to work . I only have a Kobo and a Kindle that do not even use the same formats )
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