I've lost keybindings after an update previously. I've lost ALL of them, so I'd just restore from my backup so that's no problem. However, when I just lose some of the key bindings that's a bit weird. Fairly recently - this year - there had been an update and everything was working just fine, until I tried to use one particular button and it didn't work. That single binding had been removed during the update. It was something like Heatsink or Chaff I can't recall exactly, but the binding was empty so I just added it back again.
Ages ago, I was given a tip to always ensure my stick is connected when I launch the game. There were reports of people firing up the launcher, then plugging in their stick and losing bindings . So now, even if I'm just updating the game, not playing it, I'll plug my stick in and just that stick, and other than the loss of that single binding, I've not had issues.
I have a double back-up of my bindings in effect. I make a copy of the file of course, but I also have a diagram of my X52 with the buttons labelled, in case I ever have to re-create them from scratch. Also good to have a visual reminder when I've not played for ages.
Scoob.