A friend of mine called the customer support and got a mixed answer on this question.

I'm looking at harmony 890 or 1000 to control all the home theater systems in a house. The components are going to be in a closet located on each floor and I wanted RF so I wouldn't have to run extenders to all the screens or worry about pointing the remote at a receiver for the 5 seconds it takes to transmit.

I understand that the RF remotes pair with the receiver, but I wanted to hear from someone out there who has done multiple Harmony RF remote systems. Have you experienced any interference? All my screens are the same brand so if I turn one on will all the TV’s in the house come on? Does the pairing eliminate this? Does it work like bluetooth device pairing?

Thanks
Bently

Bently - you should have no conflict, however, there may be limitations between the H1000 and 890 being on the same account. The 890PRO should allow multiple remotes and RF Extenders, whereas the 890 is limited to 2 RF Extenders (maybe more).
As with the Z Wave protocol, only the primary remote can add new RF devices (RF Exteners and lighting modules) to the RF network, but secondary controllers can be added. I'm not sure if the Harmony platform is supporting multiple remotes at this time, but you might check with their customer service
EL