Logon Script - Migration of users between Win2003 TS and Win2008R2 TS

We are migrating from users from Windows 2003 TS/XenApp 5 to Win2008R2 TS/XenApp 6.5.

Currently in user's AD properties they have a logon script (logon.bat) set. This script runs when users log into their local workstation and also when they log into Win2003 TS.

We're going to migrate users over in groups and part of that migration was to remove their 'logon.bat' and put as much of the logon script into GPO Preferences however there will be times when users need to log into both environments.

To save us removing and putting logon.bat in each time users switch between environments, how can we leave the logon script for the Workstation and Win2003 TS environment and bypass the logon script when they log into the Win2008R2 TS environment?