On Garmin Edge devices, there are TWO tracks — the one you are following (Garmin calls this a "course"), and the one you are recording (your recorded "track"). They are SEPARATE. You can change the navigational-track — the "course" — as many times as you like, this will NOT affect your recorded "track".
So, I have a Garmin 1000. I will press Start in Loughton with track N1. At St Ives I will select course N2 and carry on. At Spalding I'll select N3 and follow that. Etc., all the way to Edinburgh and back again. I will follow 20 courses (17 if you're using the official GPX files), but I will record only one single track of the whole event, all 1400+km of it.
There is a trick you need to know for audax: the Other Button — the Lap button! The button next to the start/stop button is the lap button. Now, I KNOW we're not doing laps, but the beauty of the lap button is that it restarts certain fields while not affecting others. Therefore, when I leave St Ives, I will press Lap and my "Lap Distance" field will return to zero — and so the distance in that field will accurately reflect those contained on the routesheet. I measure my progress on the lap with the Lap Speed field — the average speed, but only for the current lap. Next to that field I also have "Average Speed" and this is the overall average speed of my entire LEL workout, from the beginning, and includes all the stops (Edge does not give you a moving-average, only an overall-average). And there are other Lap fields. Remembering to press Lap is the hardest part, the rest is all in how you set up the fields on your display.
And setting up the fields is an art in itself — I have a pair of data screens that I have become comfortable with over the last four years, riding quite a few brevets: one contains all the fields I use all the time, the other contains fields I check every now and again, and I flick between the two as I need to. If you're heading straight into a Long One without having sorted these out for yourself then expect to be fiddling with these fields as you're riding to find a set that help rather than hinder.
Now, JUST TO BE CLEAR, you have to be careful on Garmin 800/810/820 devices — these earlier models CANNOT record more than about 340km reliably and are almost guaranteed to crash. Instead, with those devices, you must regularly stop your recorded track and save it and start a new track, every 300km or so. This is a device limitation on certain individual units (like my 800). That's okay — it is possible to stitch all 20 recorded tracks back together when you get near a computer, before uploading to Strava.