No. Awake is the state you are in, here it is acting as an adjective and not a verb. The verb used here is actually ‘are’, so you would change that to its past tense, which is ‘were’ and keep the adjective ‘awake’ as it is.
So, “क्या आप अभी जागे हुए थे ?” gets translated to:
Were you awake right now?
Although it is a literal translation, remember that ‘right now’ should never really be a past tense. But because of the way we speak it in Hindi it sounds OK.