[dev]

A second BES 4.0 server in the Exchange 2003 environment will require that those users recradle. Also, maintaining the old BES in the Exchange 5.5 org increases the administration effort, not to mention the eventual migration of those users from Exchange 5.5 to Exchange 2003. That amounts to doubling the work effort.
The simplest option might be to export and then import the users onto a BES 4.0 in the Exchange 2003 org. This BES would use the same SRP ID and Authen keys, so that the users are not inconvenienced with re-cradling. The numbers of users would be important to know before hand to kind of gage the effort and time required to complete the process.
If the users are already scattered, but all on one BES in the Exchange 5.5 world, it's not going to be a major leap to maintain the same scenario for the new BES 4.0. As a matter of fact, scattered users will be least of your worries if you can replace it with ease of administration and deployment.

If two different orgs, then you'll need two BES servers (missed that part)