The reason for this is that with Bonjour there is a direct high-level network connection between the two devices and their respective file systems and the DEVONthink databases and there is no intermediary set of sync files to “clean”.
You mention using “multiple methods” for workaround. What did you do? That might provide some insight. @Bluefrog’s suspicion about just having to wait for the queue of syncs to occur makes sense to me, as a starting point.
If the issue bigger than simply waiting for the data to move (nothing is instantaneous), perhaps look at
again. Also, maybe your local network router (the box that creates the network) needs a re-boot or something.
Finally, with a support report as invited by @bluefrog can more effectively help, for sure.