Another option would be, to generally allow 'outsourced includes' for every section in the main wwwoffle config, like with purge.conf and dontget.conf. The upgrade script would still only would handle the main config, and leave the includes uintouched. Then you can switch (by ip-up or whatever) some of the includes rather safely.
Assembled configuration is what many projects with growing configuration volume did in the last few years, like apache and exim4, or xinetd. � /\/
