load just the mod you want cleaned, then there is a clean masters that will remove all masters that it doesn't need.
At work so can't tell ya the step by step, but it's in there (and likely documented).
Thank Mortvent.
I went through the Traning manual (Miax's) and it also noted the 'Clean Masters' command.
Unfortunately it doesnt seem to work.
I have deleted all the Calibr references, have checked in FO3Edit (it still shows on the list when I try to load only my mod), and can see no remaining shared references.
Right clicking on my mod and selecting "Clean masters" seems to have no effect, and when I close the app there is not save message.
I guess there must still be some hidden Calibr trace.
How can I find and excise it?