No there isn't a good way to combine two previously separate apps into one universal one. I think the standard approach is just to submit the universal one as an update to the more popular of the two, to minimize disruption for users. Then for the one that is being orphaned you can push an update that nags them about the new universal app and directs them to the app store to download it.
If it's a paid app, there's really no good way to avoid some users having to pay again if you need to support only one app going forward. For a tiny number of users there are promo codes, or you can offer it free for a limited time unpublicized except by a notification in the app being obsoleted, etc. But none of those are really good solutions.