Hi Niels,
I take it you use the "Add all methods" button of the Consume REST API pop-up? In that case it's indeed not possible to refresh the existing API. I agree that's quite annoying. If you've added just a single method, the only thing you can do (safe for deleting/adding the whole API) is manually adding that one method.
EDIT: I just saw this idea, that's basically what you want.
I take it you use the "Add all methods" button of the Consume REST API pop-up? In that case it's indeed not possible to refresh the existing API. I agree that's quite annoying. If you've added just a single method, the only thing you can do (safe for deleting/adding the whole API) is manually adding that one method.
EDIT: I just saw this idea, that's basically what you want.