There is a bug that appears to address this issue that should be fixed in the 7.x release.
CSCsz93658 Copied maps are seen in virtual domain even if they are not assigned.
The underlying issue seems to be that the virtual domain/paritition is showing maps that are not assigned to it. Whether or not it will resolve the map view when integrated is the question.
You may want to talk to your account team about a PERS to see about making sure that specifically gets addressed if it is a business need which it sounds like it is.