Obviously this is a crazily long distance and one would not plot as a single route but is it really as simple as follow section 1 to control and then load section 2? Does this interfere with the ride data captured or not?
The ride data captured is unrelated to the gpx track you are following, so you should be able to load each section as you need it, while recording data for one long single ride.....
*However*, I would strongly advise you stop recording ride data at the end of each section, & start a new recording for the next section. It is very easy to join the '.fit' files together once you are back home (free online tool....
https://www.fitfiletools.com), to give you one single file for the whole ride. (Note that the route sheet gives you accumulated km for the section you are on, not for the overall distance, so this would also help in matching your device data distance to the routsheeet distance while you are riding).
I did WCW last year, used a Garmin Edge 800, & tried to record a single track/data file for the entire ride. Unfortunately it crashed after 450 (ish) km, & I had to reboot it, at the same time losing some of the ride data I thought I had recorded. It turns out this is a known issue with the Garmin Edge 800 - it can't record a single ride data file big enough for a 600 k, but I didn't know that at the time.
I have a Mio Cyclo 315 now, & tried to do the Severn Across last weekend by following a single GPX track on it. This was a disaster - the huge size of the file meant the device kept hanging, especially when I diverted off route for a few metres & it tried to re-route me back on the track - it clearly can't cope very well with big GPX files. I ended up having to reboot the device many times during the ride, & lost a lot of my ride data as a result.
So my advice is - use small GPX files, & record small ride data files, 1 for each section.
Hope this is of some use