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If not, this might be a bit overkill, but the combination of 'vJoy' and 'Joystick Gremlin' should do the trick. It's meant for use with joysticks, but there shouldn't be much difference between them on a device level.
vJoy creates virtual gaming input devices, which Windows will handle like any physical device you connected yourself. You would simply create a device with the same amount of axis and buttons as your physical controller.
Joystick Gremlin maps input from physical devices onto vJoy created virtual devices. It can also do all kinds of tranformations on the way. Like introducing secondary layers by holding/tapping a modifier button, switch between different button configurations, change axis-parameters and a lot more.
While the tool is quite powerful and comlex, doing things like swapping a button is relatively easy. You will basically decide for each physical button which button on the virtual device gets activated and be done with it.
Read the documentations for both programs carefully (only as far as you need).
You might also need a third program to hide your phyical controller from the game in order for everything to work correctly. Some games just don't handle controllers and sticks well or simply refuse to let you choose which device they should use.
In case you need this, one of the documentations (probably Joystick Gremlin) will detail your options.
There are definitely easier options out there, but I don't actually know about the, as I was orinally searching for something that does the more advanced stuff that Joystick Gremlin provides (You could try one of the programs it mentions on its' frontpage, like autohotkey).
https://whitemagic.github.io/JoystickGremlin/
I'm not be able to really look into this ATM, but I still wanted to say thanks for the detailed response.
Edit: and by Raft I mean Subnautica. Forgot what forum I was in. Oops.
Thanks, this is really good to know. I tried the record method when I first used the software, but it seemed weird so I pretty much ignored it from then on. Kind of like the built-in help.
Unfortunately due to the issue with the right-stick, this isn't really workable in this case. I'm not sure if I've ever left the right-stick as right-stick for any other game though, so I can't say for sure if this is a Subnautica bug or something deeper.
Unfortunately, DirectInput mode has its own suite of issues. I've used it effectively when I had to remap the entire controller to kbd/mouse input. But it seems to be an epic failure when you still want it to be a controller.
I tried this (just the swap) with another game and it was even worse. Both sticks had issues, buttons at default did different things, and to top it all off, the remapping didn't even work. :/
I eventually managed to get vJoy+JG (plus HIDHide) set up and configured with A/B swap. However, I could not get the D-Pad to work at all when remapped as a D-Pad (aka "Hat"). According to JG docs, the vJoy must be configured with 4 D-Pads, so I did try assigning the physical D-Pad to each one. Eventually I used another feature to make each direction behave like a button.