The command which was run during the version update was the built-in passbolt cleanup which was run with the --dry-run flag to show problems to you so you can optionally check before actually fixing.
The full command without the flag and run by your webserver user would be something like:
sudo -u www-data /usr/share/php/passbolt/bin/cake passbolt cleanup
If you run the base passbolt command without cleanup you will see other available commands.