Combine two applications

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.

Thank you for your answer. I thought so but i wanted to be sure. This application is paid so i guess that couple of people will be angry (and I understand them).

You can make a bundle of the new app and old app, so that anyone who puchased the old app can complete the bundle and get the new app. Price the bundle same as the old app.

I have a similar situation but for tvOS. On ATV3 I have two apps. The powers that be now want to join those apps together into a single tvOS app. both apps are pretty similar but are distinct apps in that the datastore are completely separate. How do I go about packaging them both up into a single package? I know I have to write some boot strap code in main.m or someplace similar to do the app switching. Just not sure what the best practice to do so is.