Yes. A Soldier can absolutely be flagged while in a deployed status. If the threat of enemy action is possible the session should be delayed until it can be handled during a period of reasonable safety. Remember: only Commanders can initiate flags. NCOs may recommend a flag action.
A word of caution
I strongly encourage you to discuss the potential flag action with a senior leader in your chain of command prior to discussing the flag action with the Soldier. This especially important while deployed due to the significant stress involved during a combat deployment and the possibility that the Soldier may have easy access to weapons and ammunition. You want to ensure the discussion is conducted in a professional manner and does not cause the Soldier to react in a negative or violent manner.