You need to remove the corresponding publication item (mapping the table in question) from the publication to remove the table. The synchronization will pull down all the tables in the publication to the client side. To remove the publication item, use either the MDW or Consolidator API.
Oracle Database Mobile Server team
One more note: After you make modification to the publication, you need to do a complete refresh. A complete refresh can be triggered via: a) delete the databases on the client side and sync again, or b) set the complete refresh option on the mSync program.
Thanks, Complete refresh was missing.