The media report in The Irish Times I read said the Captain of the UK registered fishing boat declared a "PAN PAN MEDICO" on VHF radio relayed by the Irish Coast Guard which allowed him to talk directly to a doctor at the hospital. The doctor advised the Irish Coast Guard based on the information received from the Captain. They must have understood the thumb to have been severed to warrant evacuation by helicopter. But it wasn't severed, and thus it was open for the fishing boat to proceed to port.
It turns out this same fisherman was injured, and evacuated by helicopter from another boat, in the North Sea nine months ago. Fishing is obviously a dangerous profession.