Apples sync services known to be unreliable. Have you turned it off?
Did you set up the Bonjour exactly as instructed in the DEVONthink Manual, page 61 of the 3.9.2 version? Also review Bonjour Simplified
What was the error messages when hooking up Bonjour?
Also I recommend you do a verify and repair on all the databases, and empty Trash.
Finally see the section in the DEVONthink Manual on troubleshooting sync issues, page 188 of the 3.9.2 version.