An island can have a long afterlife underwater
The Hawaiian-Emperor chain contains a long sequence of volcanoes, many now beneath the Pacific. USGS describes how plate movement carries volcanoes away from their source of magma. Erosion and subsidence can eventually reduce an island to sea level and below. Reefs may grow around a sinking volcano while conditions permit; submerged flat-topped features are called guyots.
This is a real route by which former islands disappear from a modern map of dry land. It does not require a nation, a city or a sudden catastrophe.
Sources: s1
Geological age and human age are different clocks
A rock date concerns the formation or later history of that rock. It does not date a house built on it. USGS's account spans millions of years of volcanic growth and change. Importing a geological date directly into a settlement story would leave the human occupation untested.
Sources: s1
The evidence we would need next
A drowned-settlement investigation has at least three distinct questions: was the site once dry land, was it habitable, and did people occupy it? A seabed survey might help answer the first. Freshwater availability and a reconstruction of the relevant shoreline would help investigate the second. Securely identified, dated material in its archaeological context would be needed for the third.
Keeping those columns separate makes a lost-world story more interesting as well as more honest. A location can be geologically plausible and still lack evidence of inhabitants. In the fictional collection, we can choose to imagine those inhabitants; in a reference article, we must leave that column open until evidence fills it.