Population crossed at much earlier date, when Med was lower than today, perhaps short haul, line of sight, island hopping.
The future population had enough sense to move their community to higher ground as water rose to points higher than today, rather than drown.
The higher water reduced total area of island, reducing carrying capacity; climate would also be affected, maybe adversely affecting traditional food sources, so population became to low to sustain itself, and died out?Fresh water sources became scarcer?
Rising water & sedimentation joined in wiping out any trace of earlier, (and probably still submerged) lower sites?
Maybe “artifacts” are misinterpreted?
Humans have navigated open water for at least 800K years. No one walked to Crete, ever.