In the GPOAdmin console, a user with sufficient rights can execute workflow actions "at once". Imagine the following scenario: A user with admin rights can directly "deploy" a checked-out GPO from the console. The console will then conveniently check in, request approval, approve, deploy and finally synchronise. If the synchronisation targets are modified in any of these workflow actions, the GPOAdmin console will not pick that up when it finally executes the synchronisation. Reason being: The console creates a list of all synctargetinfo of the current item at the very beginning of the deployment process instead of immediately before the synchronisation workflow.
Submitted an enhancement to change when the synchronisation targets are read during the deploy administrative shortcut to handle the case where we change the target list just before the deployment step via scripts.
The enhancement ID to be considered for a future version of GPOADmin is 585431.
Additionally, there is a workaround for this at the moment. If you use the administrative shortcut to request approval, rather than deploy, you can then approve in the console and deploy. This would separate the approval and deployment steps, allowing the script to update the synchronisation targets before deployment of the GPO.