@iandaemon yes, that’s pretty much it. Emulation station writes a configure file for retro arch and other emulators. If you change a button in retro arch, say you like to use y and b as your a and b in Nes per say, and reconfigure, it doesn’t effect the hot keys. Those are still mapped to the original emulation station setup. So let’s say you move start to say, R1 in retro arch, start for the hot key will still be the original start you chose in emulation station.
Please do not post a support request without first reading and following the advice in https://retropie.org.uk/forum/topic/3/read-this-first