Sorry, I can’t reproduce it. Did you check owner and permissions of /var/www/html/freepbx?
[root@testserver ~]# ls -l /var/www/html
total 8
drwxrwxr-x 3 asterisk asterisk 54 Oct 10 21:44 freepbx
You are absolutely right. Reinstallation should work better in your case but I’d like to know why it doesn’t work so we can improve Nethserver.
Could you post relevant error messages in /var/log/messages after trying to install/remove?