Unfortunately, it looks like your issue is different than the one mentioned above and I'm not able to reproduce it.
In order for us to further investigate this, can you please send us the following resources:
- the old .AIP file
- the new .AIP file
- the Updates Configuration Project
by email to support at advancedinstaller dot com
And also could you please give me some more details about how to reproduce this issue, a test case which I can follow in order to reproduce the problem?