Found a solution. In Documents\STAR WARS Squadrons Steam\settings there is a file: ProfileOptions_profile_synced
I was able to edit that manually. When I relaunched SWS, it said I was unsync'd with the cloud but gave me the option to upload my local version. Worked. Below are the exact edits I made. There are also some sensitivity and deadband options which could be useful.
1) towards the top of the file are entries:
GstInput.JoystickDevice1 MFG Crosswind V2
GstInput.JoystickDevice2 Joystick - HOTAS Warthog
GstInput.JoystickDevice3 Throttle - HOTAS Warthog
GstInput.JoystickDevice4 MFG Crosswind V2
I changed it to:
GstInput.JoystickDevice1 Joystick - HOTAS Warthog
GstInput.JoystickDevice2 Throttle - HOTAS Warthog
GstInput.JoystickDevice3 MFG Crosswind V2
GstInput.JoystickDevice4 MFG Crosswind V2
2) Then I did a few simple search and replace operations:
Search for "deviceid 2" Replace with "deviceid 9"
Search for "deviceid 0" Replace with "deviceid 2"
Search for "deviceid 1" Replace with "deviceid 0"
Search for "deviceid 9" Replace with "deviceid 1"