Although the regional variant of Spanish I am used to would use "estabas" 99% of the time in your example, it doesn't really matter with this verb, estar. Basically, if something is or was ongoing, then use the descriptive past (estabas); if it's more pinpointed, then use the time-delineated past (estuviste).
But let's change the verb and see what happens:
A. ¿A dónde ibas?
B. ¿A dónde fuiste?
In A, we set the scene, for some sort of interrupting action, for example, Where were you going [when you remembered you left the stove on]?
In B, the going has been completed. A possible context for this question could be: the person went somewhere, arrived, left again, and returned to the point of origin (home, place of work, restaurant where this person and the interlocutor are having dinner, etc. This question is equivalent to Where did you go?
So in situations like this, it does matter.