The Method RegisterApplication defines currently:
RegisterApplication will create duplicate records if the ApplicationUri already exists since misconfiguration of applications can result in different applications having the same ApplicationUri. Before calling this Method the Client shall call FindApplications to check if a record for the application it is using already exists. If records are found which appear to belong to different applications (e.g. the DiscoveryUrls are different) then the Client shall report a warning before continuing.

Following problems:
(1)
It makes no sense to create duplicate records for the same ApplicationUri. This creates basic problems, especially if signed certificates are handed out for the different applicationIds.
We should completely disallow duplicates.
A adminstrator need to fix the issue and find the reson why duplicates exist.

(2)
We say the client "shall call FindApplications" and then "the Client shall report a warning before continuing". But what is continuing. Use existing entry, call UpdateApplication.
And what happens if UpdateApplication puts the record on a real duplicate application. Is it required for the GDS to invalidate all signed certificate for the old one?
This is a major problem if the ApplicaitonUri is used by different application