If you have sifa on and fail to acknowledge in time it will quite literally brick your train bringing an abrupt end to your service. There is no way to release the brakes in which your only option is to quit.
You have to press the HLL refill button on the right of your desk, next to the right Ebula screen. That will refill the brakes, then you can go again
Thank you very much for this information, because I am also in such a situation and did not know what to do. Edit: https://forums.dovetailgames.com/threads/recovering-from-emergency-stop-ice1.58348/ The topic was also described here.