There have been a few times where the overnight HRV hasn't synced from my watch to Garmin Connect. I've checked the app and website and the nightly average is displayed but the graph is empty, and it says there is no overnight HRV data. The graph shows data on the watch in the HRV glance / widget.
I have multiple watches and the one I wore last night isn't set as my primary wearable, and the sleep and HRV data synced to my other watch and displays on it so, the data must have made it to the server, or at least the app so that it could go to the other watch. I've changed the setting for my primary wearable and will check tomorrow if the HRV graph displays on the graph on the website / app.