gwneud doesn't take yn, though, to my knowledge. If anything, it would be Wnaethoch chi fwyta yn y caffi preifat? if you want the meaning "Did you eat in the private café"? Note the soft mutation of fwyta after the short-form verb wnaethoch chi.
But o'ch chi'n bwyta is "were you eating?" or "did you used to eat?" or, if you insist, "did you use to eat?". (The correct spelling of the question form of this slightly colloquial form is debated.)