Not sure if this is possible or not, particularly with newer versions of maya as I'm stuck on 8 here at the moment but is there a way of replacing multiple refs all at once? i.e. replace all refs of sphere_01 in a scene with sphere_02.
I noticed that using reference>replace reference works for a single ref, but the name doesn't update in the ref editor even though the mesh changes in the viewport which seems odd.
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This is in Maya 2008 though, not sure about Maya 8
As for replacing multiple references, I'm not sure, I've never had to do it - sounds like a simple thing to script, though.