If I understand the question: you don’t have to choose between idempotence and efficient incremental updates if you can give your application data a revision number. Send your incremental update(delta) with a reference to the app data’s last revision. Increment the revision number after applying each delta and reject any delta that doesn’t reference the current version on the server, they’ll only be applied at most once, so they’re idempotent.

There are fancier versions of this scheme that can be devised based on the business rules for your application.