I uninstalled the plugin before I could check but I doubt the files were moved anywhere before that because the size of the WP installation on the server-side dropped from 1.25 GB to 0.75 GB. Plus, the subdirectory would only serve part of the problem given that the reference to the files were also deleted (eg. I had to code back the path to the logo on the main page).
Too bad my auto-backup and performance cache failed me on that one – I found out about the damage once my roll-back version had already been replaced with a bad apple.