I used to have an issue when the keybindings changed between the old patch and new patch. I think it was the new throttle system. some imported keybindings didn't work, while other worked good. What happens, button x is stock on binding a, button x gets bound to binding b. You get 2 modifications in your keybinding xml. The first where button x gets bound to binding b. the second where binding a gets cleared.
If saved bindings are different from new bindings, this can lead to problems. Cuginos solution works the bets then. First, reset all bindings to default, then start removing all bindings and bind them new.
I was trying not to have to do them all because it took me sooooo long to do it the first time
I can feel your pain, but it works the best. At least you know which button has to be which binding. If you don't know it, then probably you didn't use that binding regular, maybe a button that is free for a more important binding.