Just to clarify, I am using Harmony smart control and elite universal remotes.
I have been doing more reading and found that since Harmony's database already has codes for FLIRC/FireTV and FLIRC/Shield, there is no need to reprogram anything using FLIRC software, is my understanding correct? (see option 1 in this article: https://mediaexperience.com/flirc-remote-control-companion/).
I have 8x8 HDMI matrix with 6 different devices connected to it, two of them being Shield and FireTV. Currently if I am on FireTV activity, and press right, left, up, or down keys, it also does same on Shield device. So, somehow both devices appear to understand same set of codes. Not sure how can I fix this.