Thank you for your post!
As you mention, using multiple files with the same name is bad practice. I was also unable to reproduce this issue on Mac OS X or the Windows Operating System with FileMaker Server 15.0.2/15.0.3. To attempt to reproduce I followed these steps:
1. Created Additional Database Folder Path
Mac: filemac:/FileMaker HD/Test/
2. Uploaded Test.fmp12 to the Additional Database Folder (Using FileMaker Pro 15.0.2)
3. Attempted to Upload to the Main Database Folder Path (Using FileMaker Pro 15.0.2)
-Received the "File already exists on server" message
Did you place these files in their respective locations manually (without using FileMaker Pro) or do you have further information necessary to reproduce?
That is peculiar. I tried recreating the problem using the same combinations as you and failed: The server log correctly states that another database of the same name exists already and refuses to show it in the list of available databases. I used a mix of subfolders in default subfolder, folders in other locations and other disks but it worked as expected. I wish had done a quick movie of the problem while it existed.
On top of it I tried to add a runtime version (same name, different prefix) of the database which is - I think - how the original problem may have occurred. This is also handled correctly.
Since I can't recreate the problem today it must have been caused by a unique set of circumstances that fortunately didn't persist.
Sorry for troubling you and thank you for getting back so quickly.
André Just Vedgren
The issue was reproducible at the time I replied. I did report the issue and it seems it was resolved. To my understanding something on the Web side of things just needed to be updated on our end.