Alright I think I found my answer here. Sounds like Harmony profile sends same IR signal for FLIRC profile. So to get around this I need to pick a random profile for a device I don't have and program the FLIRC GUI manually for the second FLIRC.
Here is key notes from this thread for me:
Flirc doesn't have a notion of activities on your remote. It doesn't know which activity you've selected. What we've trying to tell you is that:
You choose two device profiles you set up on your remote. It can't be one of the Flirc profiles (like Flirc/Kodi or Flirc/FireTV etc) because both Flircs are going to respond to these. You can, for example, select an LG TV for one Flirc and Panasonic TV for another. You should also take into account what actual devices you own. So if you actually have an LG TV then don't use that one for Flirc, because both your TV and the Flirc would then react at the same time.
After you've chosen 2 device profiles you want to use for your Flircs, connect a single Flirc to your PC, select one of the profiles on the remote and use Flirc GUI to map buttons on the remote to functions/keyboard shortcuts you want to control your FireTV.
Disconnect first Flirc, connect second one and select the second device profile on the remote. Repeat button learning, but this time for functions to control your PS4.
Use these two device profiles in your Harmony activities anyway you like.
I'll try this tonight and update.