I believe that normally such a task would be done using a pre-filter on the info map (i.e. based on logon id's).
In my understanding within the metadata data model objects are linked over id's. Therefore replacing an info map means creating a set of totally new objects (even if they have exactly the same names). As these are new objects nothing will link to them.
BUT: If you import metadata (from an .spk file) linkage happens over names!
Something like the following could work (using SMC):
- Make a copy of the info map.
- Export the WRS reports (without dependencies)
- Import the WRS report into a new folder and select the new info map.
- Using IMS modify the new info map the way you need it.
This should duplicate the WRS reports and link the duplicates to the new info map.