Joel Priddy (`cephalothorax') ponders Apu-Punchau's eclipse, coming up with two solutions, one involving Severian bending time, the other involving the ship Tzadkiel reflecting the wrong part of the sky.
I think it's much simpler. The ship is large and opaque, and passes between the sun and the stone town for a while at and after sunrise, then leaves. By the time the sun is revealed, stars that are normally obscured by daylight at that season are visible (which is how the townspeople know that the night has been prolonged).
This seems to me to be the explanation that Wolfe hints at:`the passage of some opaque body between the Old Sun and Urth' (The Urth of the New Sun, p. 371).
It's interesting that the event is miraculous from the point of view of the townspeople (regular astronomical events have been perturbed) but is explicable in terms of plausible physics (the interposition of the ship). The ship, however, is run by divine beings who are acquainted with Severian's special role, so we're back to miracles again!
-- Dan Rabin