I'm not entirely convinced that the Defiant ever returned to interphase, or that SCE: Interphase, Parts I & II should be regarded as still being in continuity.
Ahh, but note that the insignias of the
Defiant crew in "In a Mirror, Darkly" are based on the Starfleet Command "boomerang" insignia from TOS (as seen on the "racing stripes" on the side of the
Enterprise and its shuttlecraft), whereas the insignias on the
Defiant crew in "The Tholian Web" are the same arrowhead insignia the
Enterprise used. Mirror-Archer was right that the
Defiant came from the future of a parallel timeline -- but that doesn't mean it was from the Prime timeline. Maybe it was from a very similar parallel reality.