Can Microsoft Flight Simulator use two identical joysticks

My answer to this would be “no”.

This is an issue I came across when developing Aircraft Specific Control Profiles and Preset switching for Aircraft Manager for MSFS 2020 - Sonicviz and I have on my “Known Issues” as

  • Duplicate Devices: Does not handle duplicate devices with same Device name. This is a MSFS bug that needs to be fixed

You can’t change the names. Basically what’s happening is presets you set for one will occasionally pop up in the other one named the same, because they are referenced by the device name, not the unique USB identifier each device should have to make them distinct. Some other users have encountered this as well, as duel devices are common in space sims, eg: Twin flightsticks for ED/SC etc.
So even if you make distinct preset names at some point they might just randomly switch. Fun eh!

I see on the latest developer roadmap they have now said their own implementation of Aircraft Specific Control Profiles has moved from “under investigation” status to “planned”, but no timeline.

They will no doubt come across the same bug, and have to fix it at some point when doing the implementation.

Alternatively, you could try changing the device names in Windows and see if MSFS detects the different names. Consult the google to see if that’s feasible, but be careful. I don’t have two duplicate devices so never got to testing that theory.

Edit: or, yes, you could try naming presets uniquely for each device which will then show up in each, but there’s potential issues if you reconfigure phyiscally as well.

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