From my understanding there are just two options available.
Create the Root/Host certificate for the IPSec server from scratch, replacing the old one. That will cause all your existing client connections to be removed and require fresh creation. Not a good option if you have a large number of clients set up.
The other option is to make a backup and then edit the /var/ipfire/certs/serial file and replace the 01 with a 02
The second option is the one mentioned in comment 4 in the bug report and allowed the Root/Host certificate set to be renewed.
The backup ensures that if something does not occur as expected that you can go back to your existing situation.
EDIT:
With option 2 the WUI renew function still does not work after incrementing the number in the serial file. Error messages are still produced.
What you have to do is the following, both on the command line:-