Sleep modes is not supported by ATOM SQ. While ATOM SQ will enter sleep mode if it no longer detects a host, you will need to disconnect and reconnect the ATOM SQ USB CABLE in order to resume sending MIDI messages. This has to be an design failure, an cheap 50 euro external harddrive has beter wakeup support than the 239 euro Atom SQ,
The Atom SQ should wake up on any pad, knob or touchstrip input. Disconnect and reconnet the Atom SQ is very unprofessional and should have been fix by a using an dedicate power button or the "setup" button (preferably any button) to wakup the device.