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I haven't tried using clsetup to do this as I would always use clrs. You should be able to simply perform:
# clrs set -p FileSystemMountPoints+=<new_MP> <resourceName>
You should not have to change anything else because the dependencies are through the resource name, not the mount points. As far as I recall, you should be able to perform this task online, without taking anything offline or disabling resources. It should be documented in the manual, but currently isn't so I'll mention it to the docs people.