Seneca is the only writer saying that an earthquake occurred at Delos shortly before the earthquake at Bura. He may have had a reliable source and others may have forgotten a smaller earthquake in the context of the larger one. Or he may have simply been confused.
Another possibility is that there may have been some confusion/conflation of similar events, specifically those of the 490s/480s BC. At that time, Herodotus reported that there was an earthquake - the first ever - at Delos shortly before an invasion by the Persians. Later, Thucydides claimed that the “first” earthquake at Delos occurred just before the beginning of the Peloponnesian War. Guidobuoni comments:
In 490, shortly after a Persian attack, Delos was shaken by an earthquake. In those days, such a matter was not without importance, because Delos was renowned for the shrine of Apollo, and so held to be exempt from earthquakes, in accordance with an ancient belief recorded as early as the time of Pindar. The particular position of Delos explains why the Herodotean tradition concerning the first earthquake was refuted by Thucydides (2.8.3). He contradicts Herodotus by maintaining that the first earthquake to be felt at Delos occurred in 431 BC, shortly before the beginning of the Peloponnesian war. According to Momigliano, Thucydides had this very passage from Herodotus in mind, and was openly contradicting him in an attempt to correct the date for the earthquake.
Jeffrey Rusten writes more recently:
Thucydides’ and Herodotus’ comments on a portentous (and unique) Delian earthquake contain the same phrase, but date the event almost 60 years apart and mutually rule out each other’s datings. Two additional problems in these passages – **geology demonstrates that Delos has never in fact had an earthquake of any significance and κινεῖν is not the word for an earthquake **– point to an explanation for the historians’ treatment. They are based on the Delphic oracle quoted by Herodotus which promised to ‘move unmoved Delos’, a paradox based on the island’s mythical transition from floating to fixed (Pindar), but liable to confusion with its equally well-known aseismicity. Normally κινεῖν τὰ ἀκίνητα is used of interfering with religious sites; but the oracle’s prediction was interpreted as an earthquake, that was assumed to have occurred in due course (although it had not). Both historians accepted the interpretation, but followed different datings since they invested it with different symbolism, Herodotus of the evils of the Persian and subsequent Greek wars, Thucydides of excited anticipation on the eve of the Peloponnesian War, since for him κίνησις meant ‘mobilization’ (1.1).
We notice that Seneca’s source is Callisthenes (360-328 BC) who was the son of Hero (niece of Aristotle), which made him the great nephew of Aristotle by his sister Arimneste. They first met when Aristotle tutored Alexander the Great. Through his great-uncle’s influence, he was later appointed to attend Alexander the Great on his Asiatic expedition as a professional historian. Callisthenes may have been the one who confused the destruction of Helice and Bura with a previous set of events, those of the 480s when there was also a great comet, possibly a Tunguska like event, a massive earthquake and a tsunami during the Persian invasion. In view of these things, one is particularly intrigued by the relationship of the comet to the earthquake taken with Seneca’s report from Ephorus that the great comet of 373 was shedding (as comets are now known to do, witness Shoemaker-Levy):
Ephorus is not someone of the most scrupulous reliability: he is often deceived, more often he deceives, as in the case of this comet, which was watched by the eyes of all humankind, because it brought about the occurrence of a major event, drowning Helice and Bura at its appearance. He says it separated into two stars; but apart from him no one has reported this. Who could have observed that moment at which the comet broke up and was reduced to two pieces? How come, if there is somebody who has seen a comet being split in two, that nobody has seen one forming from two stars? Why did he not add what stars it divided into, since it must have been some of the five stars?