(1) offer a reduced-functionality "version N" to everyone, but for the desired 'upgrade' price. (Essentially, this might only have the features of the prior N-1 version.)
(2) offer an in-app purchase unlocking full/pro features, priced at the delta between their desired "full Version N price" and what was already paid
(3) give owners of the previous "N-1 Version" a code that gives them the in-app purchase benefits for free
Maybe Apple would still object... but since the entire process happens inside Apple's system, paying Apple's commissions, advancing the use of Apple's in-app purchase mechanisms, maybe they'd be OK with it.