You can use the resetperms plugin. It will also show you which service is using each shared folder.
After installation you will see an additions tab in "shared folders" which is called "shared folders in use"
and how do i remove the reference by a service which is no longer existing? like nginx or virtualbox?
If you used this process RE: OMV 5.0 - finally out! :-) those plugins should have been removed.
Check if they are still installed and try to remove them. But do not uninstall nginx itself. If you do you will remove OMV as well as it is depending on nginx.
If the issue persists you can try to fix it by editing /etc/openmediavault/config.xml
Make a backup of that file!!!
all the plugins are removed as per post #38, apt list --installed does not show them, but config.xml still has all the old references including letsencrypt and so. getting the courage to touch config.xml manually 
all the plugins are removed as per post #38, apt list --installed does not show them, but config.xml still has all the old references including letsencrypt and so. getting the courage to touch config.xml manually
They need to be purged not removed. Removing a plugin leaves the database entries. No need to edit the database. dpkg -l | grep ^rc | cut -d" " -f3 | sudo xargs dpkg -P
ryecoaaron thanks, i did run your command, it purged a lot of packages but the references did not change:
also i am quite positive that I did purge the packages during the OMV update process.
it purged a lot of packages but the references did not chang
Output would have been handy.
apt-get purge openmediavault-nginx openmediavault-virtualbox
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