There's no problem having multiple Unity UM servers pointing at the same Exchange message store - that's probably your best bet - just upgrade the two systems where they stand with DiRT and go.
Outside of that, there's no easy way to "merge" systems together like that - I know it sounds like it should just be a snap for me to whip up a tool to do that but it's a really ugly problem to solve - there's default objects on each box that need only a single instance on the merged box and references to the depreciated objects (i.e. the ones not included in the merge of old data such as the opening greeting call handler) need to be updated to point to the new representation on the merged box - tons and tons of references (user input keys, after message actions, after greeting actions, exit actions, owners, message recipients etc...) all have to be then cleaned up after the merge takes place. This is far less than trivial and riddled with the potential to just trash your system where it stands.
As good as it gets is using the Global Subscriber Manager tool which lets you move users from one Unity server to another Unity server within the same dialing domain - you have to do this one user as a time (there's no "bulk" option here) but it does move everything in one shot for the user including their greetings, voice name, phone password etc... if you need to merge multiple UM servers this is one way to do it for user information anyway (audio text applications will have to be created by hand).
