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I doubt that sea water got high enough to get into those tunnels. It appears that they were surprisingly shallow --- and were built on the highest ground.
But, with all the rain water that apparently ran down into them, I doubt they would have been (to Epstein) worth cleaning up and restoring..
It's been reported that Epstein recently spent $27 million blocking up (with concrete?) and destroying (with explosives?) the evidence inside those subterranean "chambers of horrors".
Destruction is evidence enough and there is always the eternal record.