Actually we can only add CAD documents to a new baseline. Even if a reference baseline is set in the configuration context tab for document, the content of the baseline does not evolve after checkin.
What is your use case for wanting to update an out of date baseline, when a new baseline is going to be created with the checkin? I interpret the baseline as a fancy table representing the as stored configuration at the time the object was checked in and only the objects residing in the workspace from the assembly. We have actually configured the table view so it brings the top level primary assembly and out of date objects to the top.
The baseline is linked to a workflow process so we don't want to generate a new one during each checkin and we would prefer that users don't often and manually modify the content of the baseline if it can be done automatically during checkin. The aim is to have the same behavior as the as stored baseline but with a visible and fully usable one.
This possibility existed in Windchill 8.0 and disappeared in 9.1 so we customize this behavior.
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