I generally use “Export Data as Batch Scripts” to backup and transfer my databases, however i've also used the powertool “Database Syncronisation Wizard”.
However I've noticed that once or twice it's entirely ignored some tables (Ie left them empty)
to quote the help files:
>>>SQLyog checks for similarity in the structure and Primary Keys for both the tables. If they are not same
>>>SQLyog will skip the table during the sync process.
I shall pay better attention next time, but does it also “skip” tables with no PK?