Hi Michael;
Have you looked at the eon_offlineex object class and in particular the of_applydbupdate method? With the of_checkupdate method as well to allow the Mobile application to query the Appeon Server if a DB update is ready, the Mobile Application can then control just the SQLite DB update without itself having to be totally redeployed.
Hopefully, this might address your issue. Food for thought.
HTH
Regards ... Chris