I would not recommend using a two-way sync, as it sounds like you are doing that. Just make changes on one device, and push those changes to the other device to ensure things are exactly as you want (i.e. set the Sync Type to Update Client if the Server device has the changes). With a two-way sync, anything that is deleted will be recreated as there is no tracking of deleted entries in the database, so MobileSheets just sees that one device has something that the other device does not, so it adds it to the device that does not have it.
Mike
Mike