I’m pleased you resolved it, and have posted the reason for failure, which I have tested on our test system, and can concur, the same result is seen for failure to remove the IP address, however, in my tests it did correctly write the new IP address which was added.
I also checked and noted that the IP address which was added, then deleted, whilst still remaining in the namevirtualhost.conf, also remained shown in DNS server, and had to be manually removed.
I will forward this post as a bug so you have the credit if alright, but I know another user had a similar issue conected with namevirtualhost.conf, as of yesterday, but I did not have the time to run a check until now, so I’ll include them as well for credit.
I hope you don’t mind, but IW would not remove any additional conf you may have installed, and unless you make changes, IW does do an excellent job at updates to IW, to keep all settings as was, and I think any changes made, a backup of the original is seen, such as namedvirtualhost.conf.orig, but this also does not appear to change as above, however I could be wrong so apologise in advance.
I can certainly confirm we have been using IW for many years, and all version upgardes to IW have not stopped service (IW all version 4 upto current), however, IW do not accept any liability if your OS or Distro upgrade breaks anything, but again we have not had any service issues with this either (there has been very small issues seen though, which were very quickly correctly by IW, such as graphs not displaying, but a quick look through the forum here and you will see how many issues re updates there were/are).
Lastly, re RPAF module, have you checked to see if your downloaded file(s) are still shown, and if they are listed in conf.d folder. Reason I ask, is because you seem sure you did install this module, but are uncertain if IW would have removed RPAF, which I can only think it might only remove it from httpd.conf (if installed as module in httpd.conf), if not, then I cannot honestly see how it could remove the file from conf.d, when httpd is set to load any conf found in conf.d folder, as far as I know anyway sorry, and IW is not self healing.
I apologise if I wrong though, and hope someone would correct me.