"You can not use it to update a whole Runtime in one go. "

The Pro version supposedly does this. The free version is limited to a single folder at a time.

Worst case, you could try launching something like Dizzi's converter from your application and then controlling it. I've done that as an alternative when there was no API or command line option. I know how to do it using Win32 API calls, .NET probably has an easier way to accomplish the same thing.  

* *

"Democracy is a pathetic belief in the collective wisdom of individual ignorance." - H. L. Mencken