The good old infamous registry key will save those grey hairs.
Basically if BTS runs into any grief during an upgrade process and bombs out…this
key tells BTS setup to ‘feel free and rerun the upgrade again’

In the case of pre or post upgrade configuration failures, add a DWORD registry entry
RerunUpgrade=1 under HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\BizTalk Server\3.0_Migrated.

The setup can be executed multiple times even after the BizTalk 2006 installation.
This enables us to complete the upgrade successfully in case it fails because of some
unprecedented scenario.

More info: http://blogs.msdn.com/biztalk_upgrade/archive/2006/02/22/537344.aspx