Here as well as using 2x throttle quads and have been since release with no issues in msfs.
Joysticks would be no different as both have buttons, axis etc.
I’m trying to word it simply below, so hope it makes sense 
Windows detects usb items and assigns them unique identifier numbers.
There is a problem however.
- If you unplug one or both of the identical usb device while pc is powered on OR with the pc off, you unplug them and then do not plug them into the same usb sockets;
Windows must re-detect this “route” and reassign an id to it.
This can and does cause the “switch” in controler mappings.
The random part comes in here. Sometimes it will assign them as they were, sometimes not…
Venders use specific usb identifiers for their products, so windows knows what the unit is, but can change it from hidxxx#1 to hidxxx#2. Now msfs looks for hid1 but it’s actually hid2.
Yes, I’ve made this mistake too. My quad custom mappings remained in place but working on the wrong quads. D’ohh.
HOW TO for duplicate peripherals:
This is for msfs controller mappings only. If you are using the software that came with your stick/yoke/quad etc. this may or may not work. I don’t use them ever. Not a fan of oem software-specially Logitech.
-Use a good quality USB HUB. Powered is better then you can turn off when not in use. Plus some things require more power (led lights, timer/clock on yoke etc.)
-Never unplug anything while pc is powered on.
If you must unplug something, turn pc off first and remember to replace into the original port.
Same goes for the hub into pc connection. Turn pc off before unplugging and replace into same port on pc.
Tip: Label them for easy reference. port1/stick1 - port2/stick2
-Make sure your logged into xbox app and it is running. Required to save controller mapping to the cloud storage.
-If your Joysticks have preset mappings in msfs:
You can probably use one stick that is set on the presets if you like them, but the second stick must have different mapping, with nothing using the same function(s).
-When creating a new custom mapping DO NOT use duplicate/copy.
Start from blank + sign. Name it differently from the other one. Remember to save.
When you done set up, close msfs, reboot pc.
I usually don’t like the the presets and always create from scratch fwiw.
A common issue you might find is a “Noisy” controller can cause erratic behavior. Increasing dead zones can help, but best to use something like FSUIPC.
I have another NXT Evo on the shopping list for heli collective use and don’t expect any issues.