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If you are using 9.5 SP1 you can make it a "patch" / Custom Definition and use the "Do Not Disturb" check for file in use
If you want to leave it as a package, or are not on 9.5 Sp1, I think your only way around it would be to script or re-package it in a way that can check for file in use.
I have't updated to 9.5 SP1 (on 9.5 now). Planning to upgrade this coming weekend.
I don't have the patch management module so I assume your suggestion wouldn't work for me. Never the less, thanks for your reply!