We have a map service in ArcGIS Server whose layers are individually registered as Feature Layers in ArcGIS Online, and those items are then shared with an umbrella organisation's Open Data group to appear on their ArcGIS Hub site.
Recently, all our organisation's layers disappeared from the ArcGIS Hub site. They are still shared with the Open Data group, and we're still able to add and remove layers from that group. I tested this by sharing a dummy Hosted Feature Layer, which immediately appeared in Hub. I also changed the service URL of one of the existing Feature Layers to point to our test ArcGIS Server, and the layer immediately reappeared in Hub and then disappeared immediately when I changed the service URL back again.
An example dataset is https://waikatoregion.maps.arcgis.com/home/item.html?id=d9fb0e1a48414e7da65a6aabba79b970, which is shared to a group which should make it appear on the Waikato LASS Data Portal. The service URL is available from the ArcGIS Online item.
Both servers are ostensibly configured and responding identically, and both point to the same feature class in the same database. All I can think of is that perhaps Hub has, at some point, run into issues communicating with our production server and has cached that result and is now unable to automatically clear the issue. I've raised this with our local Esri distributor, but I'd certainly appreciate it if someone from Esri could take a look too.