We just ran into the same issues. Laurent Paume's suggestion worked in our case!!!
Within the QMC under 'Configuration System' the application storage is found under 'Engines'. Double click on your available engine. Select 'Apps' from 'Properties'. You should find 'App storage directory'.
Last update from tech support :
It's not a real bug because the app storage setting functionnality didn't exist (if you remember we changed it in the settings.ini file) that's the reason the setting wasn't migrated.
In fact, this can be problematic if you have an architecture using a SAN for example it's quite normal to change the app default storage.
Also regarding the best practices, I usually create a specific folder tree in order to get my apps in a specific folder, the external files, external qvw's, generated files... .
Anyway, it's not a huge problem as we found a pretty simple solution.
Thank you Laurent Paume. Your suggestion fixed the issue I was having.
We have around 600+ apps serving hundreds of users. I would like to know in advance all the changes needed for the upgrade. Laurent, would you please ask the support team at Qlik to add this note to the Reference Manual or to the Release Notes document?
I highlighted the change mentioned.