One way of doing it is to create a new revision from the Purchase Structure and phase out the old revision, then delete the newly created Purchase revision and obsolete the old Purchasing Structure Alternate. In addition you would have to copy the Manufacturing Structure to the Newly created Revision which is unavoidable as both Manufacturing and Purchasing are using the same Structure Revision.
Thank you dameenda for the path shown. It worked!
Just a small detail: you have to phase out the Inventory Part first, then set Purchase Structure to Obsolete and then create new revision of Product Structure.
When I was doing the steps you described, I couldn't delete or set to obsolete new created Purchase Structure.