Just checked on my pi3 ipbx, with Raspbian8
Using the fpbx gui and Admin/System Recordings feature I just uploaded a sound file and gave it a name.
I found the file in /var/lib/asterisk/sounds/custom and I found I could delete in webmin's java file manager using ie as my browser.
From Admin/System Recordings there is a feature to "Remove Recording" with the note that this does not delete the uploaded file. So 'remove' your recording to delete the fpbx reference to your recording or to your upload.
Yes a bit convoluted but you could report a possible bug to the fpbx guys.