Best way to merge tightly coupled SQL Server Instances
I faced an analogous problem where we had different environments using their own linked servers so we could never guarantee that dev was like integration was like test was like production.

The "doh" moment was when we worked out that you can name a linked server whatever you want irrespective of its physical name.

I've not got access to a SQL Server instance to test whether you can create a linked server to itself but if possible then entire redirection would be self contained within your consolidated instance until such time as you were able to weed out the procs that rely on linked servers.