Just because the cave is sealed now, does not mean it has been sealed for millions of years. Even for geology, 5.5M years is a long time. I don't understand how they can claim it never had connections to the outside, just because it doesn't have connections now.
"Combined with the geology and the peculiar chemistry of the cave’s water and air, the evidence pointed to a system that had been closed off since roughly five and a half million years ago."
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Geology is most probably largely how the sealed claim has been made .. it was open to the world when the limestone was forming, formed (Speleogenesis) by sky water (rain) permeating down and eating out a limestone void, and "sealed" by thick and impermeable layers of clays and loess (windborne sediment) some 2.5 million years ago during the Quaternary.
There are also genetic drift estimates, which put the "last" outside species to enter at about that time (
~ https://en.wikipedia.org/wiki/Movile_Cave )