the app updates are not deleted, as long as the mini-app exists it state exists, what you need to make sure is to send the mini-app in question when the disappearing messages is disabled, so if it is enabled right now for your group, just disable it, send the mini-app, and enable disappearing messages again, now the app and all its state will remain forever in the group while all other messages will be removed by the disappearing messages timer
NOTE: actually even with disappearing messages timer, an app will not be removed if it is used recently and it generated some status update, every time an app sends some status update it will refresh its disappearing messages timer, however, I don’t recommend relaying on this if the content is very important since you might lose the app if it is inactive longer than the disappearing messages timer