Seems this is before the time jump in “Life, Itself”. At one point you see at space dock, D.O.T.s putting an A on the hull. Which is confusing because we only know of the addition of programmable matter in season 3 as being a refit. However we only get introduced to Starfleet Academy in season 4.

I’m gonna say this refit happened after T’Rina and Saur’s wedding.