I'm from Kozhikode and the most interesting theory I have iss to do with floods. If you visit the museum in Kochi you will see a map displaying how the coastline changed due to floods and how it lead to formation of the island itself. The same could have happened at the same time in Kozhikode. If you look at the traditional Zamorin settlements you will see that all of them are up river in Thiruvannur, Mankavu apart from Chalappuram. It only makes sense that the port was downstream. Upstream the river would take you to Nilambur where the Teak would be brought in. The same could be done in Beypore too but without any known settlement there.

My theory is that the port was destroyed by floods and its debris making it difficult for ships to dock. There was a ship dock bridge at the beach in my childhood but it was never used back then because the beach was already too sandy. Trenching was never done either.

Also Kozhikode aka Calicut is not a dot. Beypore is very well part of the city. A lot of traditional settlements moved away after the attack by Tipu and his establishment of Feroke.