will I have to manually rebind my custom keybinding again? or can it carry over somehow since it's 99% the same hotas?
Just a guess from looking at the binding file.
Yes, unless you edit the file itself.
Each entry has a field for the device and one for the key.
E.g.
<UpThrustButton><Primary Device="SaitekX52Pro" Key="Joy_24" /><Secondary Device="Keyboard" Key="Key_Numpad_8" /></UpThrustButton>
You should be able to search and replace the device. And to remap the Keys if they are different.
It is just a text file.
It goes without saying that you use a copy and change the file name and Preset name in the file.
And the location on a PC is:
C:\Users\%username%\AppData\Local\Frontier Developments\Elite Dangerous\Options\Bindings