You will need to render two separate files. Select the first hour or less of the video by dragging the cursor over the timeline to create a blue selection region. Render this part as the first file by checking the "Render Loop Region Only" option. After this render is finished, select the second part of the file by moving the little yellow triangle that is at the beginning of the timeline all the way to the end (leaving the triangle in the middle in exactly the same position). Now render the second part to a separate file.