I currently have 2 SQL Server 2000 database instances (each running on a different physical server), each containing around 12 databases (not all are active). We are planning an upgrade to SQL Server 2008 R2, and are investigating the possibility of condensing these 2 instances into 1 for several reasons (ease of use, fewer client DSNs, cheaper licensing). The two servers are referenced by each other as linked servers (and that link is used a lot), and there are other servers involved which are also linked servers.
I understand I'll need to refactor all the stored procedures and views which reference the linked servers, but what other potential problems should I look out for? What should I check/do to determine if this is a good idea or not?