I’ve submitted a fix for the FAssetRegistry::OnDirectoryChanged case (CL# 3087216).
It was a little more involved than my earlier suggestion in order to avoid the Content Browser from getting an asset deleted event for an asset that still existed in the package (as this broke the selection in the UI).
This change also exposes FAssetRegistry::PackageDeleted to let you clear our all the data associated with an in-memory package.