I looked into this a bit more. It turns out that Metadata Cleaner was marked end of life by the owner because it's no longer being maintained. This is different from the more common scenario where an app is using an end of life runtime. I guess Discover decides to remove apps that explicitly marked as end of life.
Still, it's a poor UX to not give the user the choice. You may be able to work around the issue by pinning Metadata Cleaner, either using the CLI or Warehouse, an app to graphically manage flatpaks.