I'm guessing this solution would be more trouble than it's worth and you'd be better off re-creating any necessary objects in QS, but it's the only one I can think of. For what it's worth, we ended up re-creating everything in QS anyway without using the conversion tool, as the results were not satisfactory for direct conversion.
That's what I was thinking. The current deployment is for more than 2.000 users and all of them has the privilege of develop server objects, so, you may imagine that the manual process is not possible.
I hope that someone on Qlik read this thread and give us a workaround.
Unless you are highly confident in the quality of the conversion tool for your specific use case, I would advise against trying to do this in an automated manner. It is my understanding that the conversion tool does not get the job 100% done, meaning the imported objects may well not work as expected with the adjustments you'd have to make to the app after you've converted it.
In any case, I'll let the fine folks at Qlik speak for themselves insofar as any possible solutions. Good luck!