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You have all of your facts mixed up.

Dr. Linus didn't kill Jacob. Dr. Linus is Ben Linus from a different time period and/or reality or dimension. Dr. Linus, as far as we know, did not know Jacob, because him and his father left the island.

Ben (in the island timeline) killed Jacob in the season premiere.

Your question also assumes that Jacob has always been invisible... this is not true. The only reason why no one sees Jacob except Hurley is because Ben killed him. He hasn't always been invisible.

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