system-config-firewall is not really very compatible with manually configured firewalls. This is documented, and I have no problem with this. However, it is very easy to forget that you did a manual update and then overwrite it. When you do you don't really have documentation of the original. How about moving the iptables and up6tables files in sysconfig to iptables.backup and ip6tables.backup before writing the new ones. This would be advantageous both if you forgot that you were doing manual updates on a server, and also if you do an update and break things to put the back real fast.
Checked this with 10 and it is still an issue.
This now in and of itself is not an issue as of fc11 beta. The old versions are saves as .old files. However, if I were doing it I would also tell people that this had happened as a part of a message during the save process.
system-config-firewall-1.2.16-3.fc10 has been submitted as an update for Fedora 10. http://admin.fedoraproject.org/updates/system-config-firewall-1.2.16-3.fc10
system-config-firewall-1.2.16-3.fc10 has been pushed to the Fedora 10 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update system-config-firewall'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/F10/FEDORA-2009-5928
I think this one is ready to close and has been for several months now???
This is label as waiting my testing. My test results are found in commnet 2. Basically the problem is fixed, but frankly in a future release I would include a message saying that the old files were backed up with a .old extension. Other than if you want to keep this around and turn it maybe into a rfe I don't see any reason not to close it.
system-config-firewall-1.2.16-3.fc10 has been pushed to the Fedora 10 stable repository. If problems still persist, please make note of it in this bug report.