The fruit will reappear at intervals throughout the game, but it will never get to the amount that the tree started with. That doesn't include the effects of possible Island events, of course. I don't know how often the fruit or honey replenish but I suspect it partly depends on the game difficulty and speed settings. I do know they will replenish more often if you take the Nature path. Trees can't be chopped down.
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To err is human; to arr is pirate.