Thank you for your post.
If I remove files manually rather than using "Remove" from Admin Console, I also get the same results as you.
When a file is opened, a temporary file is also created. When you manually remove the file, the temporary file remains, and the reference to the file remains in the Admin Console. Therefore, you should use "Remove" in Admin Console to remove all traces of the file. See page 108 of the FileMaker Server Help manual at:
On my end after manually removing the file, when I restart the Database Server, all my file references are then updated to reflect the correct information.
Therein lies the problem - the admin console won't stop any of the databases, so I can't click the remove button either. Therefore, I stopped the service and manually removed the databases from the Databases folder, then restarted the entire server. The databases cannot be found on the server anywhere because I emptied the trash. They also don't show in the Admin console, but a FileMaker Pro client can still see them and open them. This is a very odd behavior and I have no way to "stop" or "remove" a database that FileMaker Server doesn't display. Any suggestions?
I resorted to using the command line fmsadmin CLOSE and fmsadmin REMOVE to force FileMaker Server to close and remove the databases. The interesting thing is the CLOSE actually closed the database, but remove threw error 20405, which is "file not found". Therefore, FileMaker Server knew the databases didn't exist on the server, but was hosting them anyway even though the server was completely restarted after the database were manually removed and the trash was emptied.
So, my particular issue is resolved for now to remove the databases, but there is another larger looming bug with FIleMaker Server refusing to stop databases or remove database and hosting files that don't exist.