Right now you can create duplicate keybindings through the Settings GUI. This can lead to some problems, like when you remap line-wrapping:toggle to ctrl+w and now you can no longer close documents with Ctrl+W even though the hint still shows this:

I can think of a couple options:

1. Add a dialog to notify of a keybinding conflict, and if the user chooses to save the new binding then it should clear the old binding.
2. Don't show a dialog, but instead automatically clear the old binding when it is mapped to another command.