Do ALL of your users want to use the linked file, and NEVER use the original files separately again? If so, copy the script from every application, resolve all problems, then copy the tabs and objects from every application, and resolve all problems. In other words, build myApp.qvw manually. I don't think there is any easy or automated way to do it.
If some users want to use them separately and some want to use them linked, the above approach won't work, because then you'd have dual maintenance. You could consider building a web page that has all three QlikView files embedded. We've worked on that with limited success, but don't have anything that users are actually using, and I don't much care for the results so far. Or you could just explain to the users that since some users want to use the files separately, you simply can't combine them. Tell them QlikView just doesn't work that way.
You may consider using the "Document Chaining" feature. This is the Action -> External, Open Qlikview Document. You can assign this Action to OnActivateSheet triggers or Button Actions. In this way you can create navigation from myApp.qvw to the other filen.qvw applications and back.
