SBmerge with three folders in Sandbox?

Hi,

I updated an App by installing some additional applications and registering three .dll's from within the App-cmd.exe.

This resulted in three folders on my Sandbox:

1. %username%
2. <actual username running the App-cmd.exe>
3. System

All of them contain files/registry data. I tried merging them one by one, but that doesn't work.

How should I merge these three folders? The snapshot containing the installed App is gone. Is there another way to update my App if I only got the project folder?

Thanks,

Patrick