Okay, massive relief.
I saved my binds yesterday using the standard method after a quick google search and finding Para's forum post. I backed the file up and have my own custom name. Then I removed the X52 HOTAS and later went back into the game to take a look. Everything was wiped to defaults. I'd earlier spent a lot of time changing all the on foot controls so, as you can imagine, my immediate response was 'NOOOOOOOOOOOOOOOOOOOOOOOO!' as I fell to my knees and ripped open my shirt.
I just tried the game again after plugging in the X52 and all my custom settings are suddenly back. Does that seem normal? It seems odd that mouse and keyboard customs like the on foot stuff are tied to a specific controller. If I wanted to change or ditch that controller for full mouse and keyboard I'd have a lot of customising to do.