I think it should be safe to manually edit /etc/sysconfig/iptables
in that case.
Of course, verify on a test system.
Also, you might be happy to know that in 4.2 we'll support firewalld,
which is much nicer to work with than patching/generating
/etc/sysconfig/iptables.
See also:
https://bugzilla.redhat.com/show_bug.cgi?id=995362