Pressing emergency stop places the machine in a halt condition, and you need to reset both the software and the machine to come out of it. The easiest ways to stop a print in a hurry is to just press “Disconnect” and then pressing the red button on the side of the machine to reset it. Then when you reconnect, everything is fine.
If you have more time, Sending “M26 M104 S0 G28” will stop the print start cooling and home it.
I will add a stop SD print button to a S3D profile soon.