FileMaker Server 15.0.2
Windows Server 2012R2
When server uses more than one folder for hosted databases, it is possible to add multiple databases with the same name - the OS will not complain. They are shown by server but all actions you try to perform on one of the duplicates will only affect the first file in the list shown in the admin console (Activity > Databases).
So if your duplicate file is actually second in the list, it is impossible to close it and remove it without removing all preceding copies of it first.
Workaround is to close first file, rename it in the OS, close and remove the second file using admin console and then rename the first file back to its original name
Yes: This is definitely an edge case where something you shouldn't do exposes limits in the functionality. But it is still a bug...