Reprogrammable Matter. Reprogram the matter so Discovery resembles what it did before. I'd prefer a retcon, and Star Trek -- especially these days -- isn't above retconning appearances, but that usually only happens between different series, not within the same series.I mean, all they really have to do now is abandon Discovery in a nebula for...some reason or another.
Oh, and I guess they'd need to undo its 32nd century upgrades, though that could be handled via just re-rendering a few shots from Calypso if they really wanted visual continuity.