Add a xantech connecting block 789-44 to the IR port outputs of the RFX9400 to expand port capacity and use stick-on emitters for the TVs if you cannot utilize different codesets as Barry mentions. Xantech CB in this configuration, should not even need a power supply.
This will be your best solution.
With regard to 'System is in use', you will need to either buy another RFX9400 and put dual emitters to all equipment the remotes need to control or live with the issue.