So i was poking around trying to find a mod for rebuilding Winterhold (no luck, all i found was a slim mod to rebuild a few shacks) and i ran into a legend that the city was summoned into being by Shalidor's whispered spell, now if this is true then maybe Winterhold collapsed because the spell expired, maybe there was some sort of ritual that was lost in time to recharge spell periodically and once it fully run out the summoned part (which i assume is the part that was around college) just simply fell.