I figured it out.
I didn't realize that syncing meant downloading all known locations of all resources.
Someone on Reddit suggested I uninstall the AddOn and if they're still there, remove the HarvestMap files from the SavedVariables folder in the My Docs/ESO folder. But when I looked in that folder I noticed the HarvestMap files with "- backup" at the end of the name. So I deleted the newly downloaded files and removed "- backup" from the original ones and I'm back to before I synced.
Problem solved.
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