Well, yes you can...one branch of a company could legally compel (and would if there are separate privacy policies) another to give up information as part of an investigation.
Even if the branches aren't distinct legal entities? IANAL, but according to Microsoft Deputy Counsel John Frank, "Courts do not issue orders authorizing someone to search themselves" [1].
You're not asking for a search warrant, you're asking to be allowed ('compelled') to look at a specific business record that groupA made but isn't accessible to groupB without permission of record_creater, UserX, or court order. Basically you're asking the court to say its OK to go around privacy or contractual obligations in order to investigate something.
I don't understand why in this case, MS couldn't have easily gotten a subpoena, anyways.