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Issue root user lost access to all vhost folders and files

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New Pleskian
After managing to screw something up trying to fix TSL issues, running a plesk re-installation/update on top of the partly working version, plus plesk repair all and more I have a working plesk installation except for on major issue "my "root" user lost access to all the subscriptions/domains files and folder on the server".

ISSUE: If I log on via SSH or SFTP my system root user can't see any folder or files inside the vhost folder. When logged in as plesk built in "admin" I can see all domain folders are there, most folder permissions are subscriptionuser : psaserv, but e.g. each sub home directly also got LOGS and ERROR_DOCS folder which owner is root:root but I don't even see those. Setting/applying permission via File Manager does nothing.

Somewhere in the process of getting things back up and running again, with SSL certificate issues, 502 pages and other issues my root user seems to have lost access to all the domains/subscriptions in the vhost folder and I don't have a clue how to fix it or even how that is possible.

My setup, dedicated server running Ubuntu 16.04.6 LTS and Plesk 12.5. Plesk repair is reporting no issues and I also tried some fix_permissions.sh provided in a support article relating to file permission inside httpdocs. I'm a total loss of what can be done, what if anything I should include here for further help on the issue.
 
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Any thought on debugging or fixing this.. my box is rather unstable since I believe the crash started with me installing nodejs via an npm command
 
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