When you create a feature layer by uploading a zipped file geodatabase or shapefile, ArcGIS Online creates two items - the original data and a hosted feature layer.
Obviously, the hosted feature layer is the item you will share with your users, so you add rich metadata to this item.
Then, when you update the layer using the "Overwrite entire feature layer" option and uploading a new zipped fgdb or shapefile, AGOL overwrites the metadata of the feature layer with the metadata of the fgdb/shapefile.
Apparently this is expected behaviour, but I would like the option to retain the original feature layer metadata.