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.
I can answer that question: histories change every time they're copied or told. Written accounts are copied much less frequently, and the copiist can compare it to the original; and sometimes you can even find the original source.
A better question –IMO– would be: how reliable are your sources? But then the writer (how in the hell is "University of the Sunshine Coast" an author?) wouldn't have had the opportunity to take an easy stab at Western history.
It isn’t — it’s an affiliation! The authors are Patrick Nunn and Roselyn Kumar, both at the University of the Sunshine Coast. The formatting on the paper is admittedly a bit confusing though; at least in my field affiliations are usually printed as footnotes or similar.
Or perhaps you would defend the latter idea as a good thing? I want to assume better of an HN interlocutor, but that would fit better with your mention of copying and original sources.
If we must "stab" something as vast and varied as "Western history", ISTM the most common choices of focus and emphasis are more questionable than the accuracy.
The research paper's history of the port seems to be largely plausible from what I can see, and it's plausible precisely because this wasn't some massive misidentification, but merely a shift from one area of the coast to another one nearby.
The Indians and West Indies thing is just about some sea travellers being dumb and thinking they'd reached India.