ok just found something interesting.. maybe you can try this
go to that users home directory and see if this file is there .wp-toolkit-ignore
check home/ and home/public_html
if found rename that file DO NOT delete it just rename to .wp-toolkit-ignore.bkp
so after we try to scan and find it - if it still does not we can rename back to the original name
just rename for a moment then try again to scan and see if it finds it this time
I found this on Plesk which is how we got the Wordpress toolkit from.
Starting from WordPress Toolkit 5.9.2 detached WordPress instances are no longer re-added through the Scan procedure, making their detachment permanent.
If the website should be added to WordPress Toolkit back for some reason, perform the following:
- Log into Plesk.
- Go to Domains > example.com > File Manager.
- Find and remove the .wp-toolkit-ignore file in the domain's document root.
- As soon as the file is removed, go to the WordPress menu and re-scan instances.
SO I would assume same for cPanel
that's why I asked if that file is in that users home / directory or public_html folder
this might cause it not to find it as stated above in Plesk statement ..