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Harvestmap saves your discovered data in the folder live/SavedVariables like every other addon as well.
If you got a backup of that folder, and especially the HarvestMap*.lua files in there, try to logout and restore those files.
If not, they might be lost. But as Sharlikran said this WON'T happen automatically. You either deleted those files manually or via Minion (by ticking the also delete SavedVars box as you uinstalled the addon).
Or there exists a bug whish should be known and fixed by now as many users would suffer from it?
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