Hey Amarnath,
Yeah, that is strange. We do the same, after a sys copy we re-import the user master records that were previously in QA. We never have the problem you are speaking about, so yes, the SAP_USER profile is supposed to overwrite existing user data.
Was your client completely open when you did the user master copy? I mean, check SE06 and SCC4 to make sure it's wide open ion the target client and that the user performing the copy has SAP_ALL in the target client.