I don’t know if this applies to your specific issue, but I’ve encountered situations on other hardware where the system recognizes the change of input device, but the emulators themselves do not. Try going into the emulator’s control settings to see if something needs to be configured there.
Steam Hardware
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Thanks - that's what I though too, but it seems to simply be this issue, at least so far. Maybe EmuDeck can't determine the controller order when booting up, and so it needs to be manually set for each session?
Either way, it works - at least for now!