I need to add an additional .pat file to detect some pattern, but I noticed that by barely adding a .pat file to the protocols directory, it will be lost on reboot.
You should download the latest protocol definitions from http://l7-filter.sourceforge.net/ and add your customized pattern. After that put it at the location /var/register/system/net/L7/l7-protocols.tgz and reboot the system.