Primary (root) blog of multisite installation forbidden (403)

403 forbidden is an HTTP error. It means the web server does not have the necessary permissions to read the requested file. There is no question about this and you should focus on this before investigating other potential misconfigurations.

Depending on the type of server you are using and in addition to resolving filesystem permissions, you may also have to resolve permission issues in SELinux if you are on RedHat or similar.

Normally, the exact error will be in the HTTP error log (/var/log/apache2/example.com-error or similar). The fact that you say you still have the error even though you moved everything back the way it was, suggests to me that file ownership changed and it is still a filesystem permission issue. To verify, you can view the apache .conf file to see what user apache is running as and make sure that that user also owns the files or is in the same group as the user you are using to move files around.

grep -R -E '^User ' /etc/apache2/* to find out what user apache is configured to run as.

If you are certain file ownership and permissions are correct, it is still possible that apache is looking in the wrong place for the files and, not finding any, is somehow refusing any access. Check the logs. That’s where the answer will most likely be.

HTH