Functionally the two editions should be the virtually identical. Legally they are not. You also have a problem if you installed the same corporate keycode on two servers.
That problem may be small if you at least own the correct number of commercial licenses. Unfortunately MS may make things a bit uncomfortable should they ever make you prove that. I suspect Windows update lets MS know when too many servers seem to have the same keycode simultaneously. I suspect MS checks its purchase records as to whether to give you the benfit of the doubt before launching a query – but if MS has a team in town anyway…. Changing key codes on the servers would solve the issue.
As far as I know everyone in a particular country and purchase program shares the same MSDN key codes. By purchase program I mean academic versus everyone else and possibly single purchase versus volume. There may be a special code for partner program copies as well. Ultimately MS is the channel for these products as you are supposed to register on their site to get the codes. I think MS started taking many volume license programs under their wing the same way for anti-piracy reasons. Basically by this handling MS gets a record of ownership and contact info if the codes show up versus too many WPA configurations at Windows updates.
It is probably better to reinstall complex server software for the same reasons MS does recommend cloning servers. The primary problem being that Exchange and other server apps sometimes record and hide the server codes in their configuration for security reasons (e.g. making it difficult to steal a corporate email database). But you can take the chance on key code changing programs if you can afford the downtime if it doesn’t work.