Unfortunately, Garmin does not notify us when you delete weight entries in the Garmin Connect app. That is why they remain in the Fddb app. You cannot delete individual entries from Garmin in the Fddb app.
If you don't want to see weight data from Garmin in Fddb at all, you can turn off the import. To do this, go to "Trackers & Apps" in the menu, press "Settings" for "Garmin Connect" and turn off "Import body stats". The Fddb app then no longer shows any body stats from Garmin, including body fat. If you turn the import back on or reconnect Garmin, all entries appear again, including the ones deleted in Garmin.