To add I think I may know what has caused this to happen on both occasions (in hindsight)
On 2 occasions, I used the “restore from back up” and on both occasions it didn’t change anything, at the time I think I assumed this was just due to autosave kicking in since the backup was made.
But now it’s happened twice to me, I think it’s actually the “restore from backup” that is actually the broken mechanic, see when my progress had not saved, I was back to the restore point in the previous session even though I had saved the map since hitting restore but it was still in the same session, when I’ve not used “restore from back up” I had no issues.