Run using navigation hasn't recorded records

Have you tried changing the type of the "Navigation" activity to "Run" in Garmin Connect?

Yes, I have changed the 'Activity Type' to 'Running', and this triggered the Marathon badge against the run, but the Personal Record remain unregistered.

This is just a wild guess, but you could try trivially editing the activity after fixing its type. Maybe change its name, trim a few seconds from the end, etc. Maybe that would trigger detection of a new personal record?

Does this mean you didn't use the running app and navigated along a course in that app? Why?

Was the distance on the watch at least 42,195km?

I used the 'Navigate' function on the watch, utilising a pre-loaded mapped 'Course' of Marathon length.

The watch distance is shown as 42.26km, so yes exceeds marathon distance.

What I think Alan meant is: is there a reason you didn't choose the Run activity and start navigation from that? Then it would have been the correct activity type from the beginning.

No particular reason .... That's just the menu routing that I've used previously when using Courses, and then assigned the activity afterwards.

This was, however, the first time that I noticed that it hadn't been reflected in Personal Records.

I am asking whether there is a way to fix this retrospectively. 

Let's hope someone knows a solution. But just in case you haven't stumbled on this (it took me a long time to realize it), it's actually just as easy to press start, scroll to "Run", then long-press left middle to get settings, and then choose "Navigation" from there.