In April of 1963, Delta Green launched Operation RIPTIDE in order to complete the annihilation of Y'ha-nthlei left unfinished in 1928.
Overview
After the loss of the USS Thresher (SSN-593) with all hands on April 10th, 1963, Delta Green personnel took note that the Thresher was sunk not far from the site of the Deep Ones city of Y'ha-nthlei.1 Although the city was thought to be destroyed, an investigation into the matter revealed this to be mistaken. Operation RIPTIDE was launched, and air-dropped anti-submarine munitions and depth charges were deployed that May to level the city to Delta Green's satisfaction.2
Background
During the raid on Innsmouth of February 1928, USS S-19 launched torpedoes at Y'ha-nthlei, and these appeared to have destroyed the city.3 However, it was merely damaged.4 Nevertheless, Project COVENANT was successful in seizing a number of documents and artifacts from the raid that contributed to many of their early victories against the Deep Ones. Yet, deciphering the Deep One's lore had unforeseen consequences, as in 1955 senior Delta Green researcher Daniel Fries suffered a mental breakdown and destroyed all of the materials seized in the Innsmouth raid.5 This loss impacted RIPTIDE's effectiveness, as much of the collected data on the Deep Ones in general and their operations in New England specifically was gone.
Speculation
Although Chaosium's Escape From Innsmouth allows for Dagon to be encountered, and the possibility of the monstrosity being slain, this is clearly not the creature's fate based on several references to Dagon in Delta Green after the events of 1928.6 This would indicate that Father Dagon is very much still alive in the modern day.7 In fact, although Y'ha-nthlei is described as being "utterly [destroyed]"8 by Operation RIPTIDE, it appears that Dagon survived even this. It is also probable that Dagon is merely a title given to the largest and most exceptional Deep One patriarch of a given clan, and not a specific specimen.
Dagon's survival is even more impressive if it is supposed that Operation RIPTIDE used any nuclear depth charges as part of the assault. It is entirely possible that Delta Green could have passed the detonation off as an underwater nuclear test, as the Partial Test Ban Treaty would not go into effect until June of that year. This would definitely give more confidence to Delta Green's claim that Y'ha-nthlei was entirely obliterated, although that confidence could be misplaced, as suits a Keeper's desires.