After some discussion at the Utrecht BSP[1], we've submitted a wishlist bug (#690390) to debconf which would make solving this bug easier. Our suggestion is to change debconf so it uses values from config files instead of its cache (the last seen answer). This means it can also no longer reset config files to their older state based on this cache. ("This file is managed by debconf" is not a valid excuse for messing with manual changes; your package is not allowed to revert user changes to config files, no matter if it happens through debconf or not.)
If our suggestions is implemented, it would be easier to solve this problem, but it would still need to allow debconf to read and write the configuration. This is another aspect of this bug: it is appearantly too hard to understand how to make the package do what you want. Pointing to documentation is not a proper solution; if it is easy to do this wrong, then it should be changed to a more intuitive method. Thanks, Bas [1] http://wiki.debian.org/BSP/2012/10/nl/Utrecht
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