Hi, I have a very similar scenario with the same issue. I have a windows media center still running (yes, I know, it's ancient, but my wife still has a bunch of crap stored in there), and I have a RPI 4 with Kodi (libreelec) installed. I use a logitech harmony hub to control all the devices. Everything was fairly easy to set up, but when I'm using the media center, the remote signals are the same for a lot of the kodi stuff, so when I'm doing stuff on media center the FLIRC in the RPI picks up the signals and does stuff. Is there a way to tell the FLIRC to "not listen" until a certain signal comes in that tells it to "turn on"?
The only workaround I've thought of so far is in the harmony software, instead of setting the device as FLIRC Kodi, use some other device, then "train" the FLIRC to listen to those signals and translate them. I guess that could work, but not for those who don't use harmony, and is generally a pain in the butt since you have to remap all the buttons / signals.