zstray,
First of all you can't upgrade major versions of software on a MiVO-250 without a license upgrade; they want their money.
The 1U unit is the older CS Controller and the 2U unit is the newer HX Controller.
The CS Controller can only be upgraded, and supported by Mitel, to version 6.1 and the HX Controller can go all the way to 6.3 SP7; which is the latest version.
Unfortunately the licensing can't be moved from the CS Controller to the HX Controller without moving the entire compact flash (CF) card. This however requires you to remove the CF from the HX controller which currently has your licensing and programming; the CF is the hard drive.
You could use the CS chassis for an emergency system down by just moving over the CF card from the dead HX controller to the older CS controller, but you may have issues if one of them has the PEC (Processor Extension Card) installed on it. If the PEC is on the CS and not the HX then you can just remove it and there would be no problems. If the PEC is on the HX and not the CS then you have a problem. In theory you could just remove the PEC from the HX controller and put it in the CS controller and your problems would be solved. The unfortunate part is that not all PECs are created equal or even identical.
In a few months you won't be able to get new licensing for your MiVO-250 as Mitel is shutting down that portion of their service in lieu of the product being discontinued. If you have 53xx series phones then you could move to a new MiVoice Business controller as they are coming out with some new smaller models later this year and you won't need to buy new phones along with a new system.
Sorry,
TE