To clarify one of the methods AlwaysConfused mentioned, a solution would be to use one of URC's RF basestations eg the MRF-260. This way, both TVs can use the case codeset, and rather than IR, the remote will communicate via RF. This is picked up by the basestation which has IR emitters attached to the IR receivers on the front of the TVs.

Using the RF settings of the URC software, the two TVs can be assigned different emitter outputs, and so it will only control one TV at a time, without changing any codesets.