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Pretty minor but you don't need the if (row_id == 0)

if (row_id++ > list_size) // Add the sublist to the result
{
    result.Add(route_list); 
    row_id = 0;
    route_list = new List<long>();
}

Also it seem like you should also test for

if (route_list.Count > 0 ) 

Why not just put where route_source_id is not null in the query?

Connection, Command, and Reader behave the same with many DB so this is pretty portable.

I think you can use

conn.CreateCommand()

Long is not required for row_id or list_size

Why bump row_id++ if there is no value?

In summary

    using (var reader = cmd.ExecuteReader())
    {
        const int list_size = 100;                
        List<long> route_list = new List<long>(list_size);

        while (reader.Read())
        {                                
           if (route_list.Count >= list_size) // Add the sublist to the result
           {
               result.Add(route_list); 
               route_list = new List<long>(list_size);
           }
           route_list.Add(reader.GetInt64(0));
        }

        if (route_list.Count > 0 ) // add the last sublist
        {
           result.Add(route_list);
        }
    }