exec sp_executesql N'SELECT TOP(@__p_0) [t].[JSON]
FROM [TableData] AS [t]
INNER JOIN (
    SELECT DISTINCT [i].[Parcel]
    FROM [IndexData] AS [i]
    WHERE [i].[Parcel] = N''some condition''
    GROUP BY [i].[Parcel], [i].[RowId]
    HAVING COUNT(*) = 1
) AS [t0] ON [t].[ParcelNumber] = [t0].[Parcel]
WHERE [t].[TableId] = 123
ORDER BY [t].[ParcelNumber]',N'@__p_0 int',@__p_0=123456

exec sp_executesql N'SELECT TOP(@__p_0) [t].[JSON]
FROM [TableData] AS [t]
INNER JOIN (
    SELECT DISTINCT [i].[Parcel], [i].[RowId]
    FROM [IndexData] AS [i]
    WHERE [i].[Parcel] = N''some condition''
    GROUP BY [i].[Parcel], [i].[RowId]
    HAVING COUNT(*) = 1
) AS [t0] ON [t].[ParcelNumber] = [t0].[Parcel]
WHERE [t].[TableId] = 123
ORDER BY [t].[ParcelNumber]',N'@__p_0 int',@__p_0=
123456

var queryResults = (from i in indexResults
                    group i by new { i.ParcelNumber, i.RowId } into grp
                    where grp.Count() == 1
                    select grp.Key.ParcelNumber).Distinct();

var jsonLookup = (from dcv in db.TableData.Where(a => a.TableId == 123)
                  join wos in queryResults
                  on dcv.ParcelNumber equals wos
                  orderby dcv.ParcelNumber
                  select dcv.JSON).Take(123456);

var jsonData = jsonLookup.ToList();

var queryResults = (from i in indexResults
                    group i by new { i.ParcelNumber, i.RowId } into grp
                    where grp.Count() == 1
                    select grp.Key.ParcelNumber).Distinct().ToList();

**It doesnt include the RowId in the query so the problem is somehow related to the join and/or the distinct**

SELECT DISTINCT [i].[Parcel]
FROM [IndexData] AS [i]
WHERE [i].[Parcel] = N'some condition'
GROUP BY [i].[Parcel], [i].[RowId]
HAVING COUNT(*) = 1