The installation records maintained by Softaculous are stored at the following path :
/home/USERNAME/.softaculous/installations.php
It looks like this file exists and it has the entry that the installation exists. This can happen if the user has not uninstalled the script via Softaculous and simply deleted the files manually.
Or if the user has terminated the services and the above directory still exists.
If the user account is terminated properly the above directory should not exist.
You can delete the above file to delete the records of the installation for that user.