It does fit a classic science fiction pattern, and you're blending together several historical and fictional motifs into one coherent narrative.
The structure would look something like this:
-
The frontier
- The Pillars of Hercules (Strait of Gibraltar) mark the edge of the known world.
- Beyond them lies a distant outpost—Atlantis as the Greeks know it.
-
The misunderstanding
- Mediterranean sailors assume this magnificent city is the civilization.
- They never realize it's merely a naval base, trading colony, or scientific outpost.
-
The hidden homeland
- Far beyond the outpost lies the true civilization, much larger and wealthier.
- It has little or no exposure to Old World pathogens.
-
The tragedy
- Explorers inadvertently introduce infectious diseases.
- By the time larger expeditions arrive, the civilization has already collapsed, leaving only ruins and fragmented legends.
As fiction, that's a compelling premise because it combines:
- Plato's Atlantis,
- the Age of Exploration,
- the epidemiological collapse that affected many Indigenous peoples in the Americas after 1492,
- and the "gateway outpost" idea used in Stargate.
