The 1790 census in Vermont is unique to other 1790 census as it was actually taken in 1791 when Vermont first became a state. This may complicate one’s attempt to research the 1790 census as an individual recorded in Vermont during the 1791 census may have already been recorded in another state during 1790.
To my knowledge there are no missing census enumerations except for the country wide 1890 census.
