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If you want Batch Patch to respect the current configuration of your target computers, then make sure the ‘Server Selection’ value is set to ‘Default / Managed’ as it is in the screenshot below.
This method also allows for the updates to be approved, distributed and reported on via WSUS.
To do that highlight the desired computers in your Batch Patch grid and select as shown in the screenshot below.
You can see the results below, which show that my targets are configured to use my local WSUS server, WIN2012R2, for their updating.
Note, Batch Patch does not modify the target computer configuration in this case.
It simply overrides the target computer configuration when actions in Batch Patch are initiated.