EDIT: The issue wasn't with HRV logging; there seems to have been a separate issue with the heart rate strap not connecting to the watch. Please disregard.
I've enabled logging HRV under System > Advanced > Data Recording > Log HRV. However, I've verified with Fit File Viewer that RR intervals are not being recorded for at least the last few activities I've done. I haven't checked every activity, but it was working as of mid-September; I think a software update since then may have broken this feature. (Currently on software version 12.72)