How to disable the option for file migration to end users?

Here's the scenario:
We have a utility that updates UNC paths in embedded files for file
migrations. The issue is when an old file version is opened, it prompts us to
migrate, recalulate, or other messages depending upon the app. We are trying
to go through 100GB of data and we can't continue to have someone manualy
click the button.

If someone know of a policy setting, macro that will work, or a code to keep
this from happening, we'll own you a big case of beer! We have tried AutoMate
which is cool but does not do the trick because each popup window has
different text including the file name.

Thanks everyone!