Comment 8 for bug 576255

A package failing to find conffiles after you delete them is exactly how they're meant to behave. If you delete a dpkg conffile, "deleted" is considered a valid "user requested state", and they won't be replaced unless you reinstall with --force-confmiss.

This isn't apache-specific, though it seems that apache users seem to be one of the larger groups of people who think that deleting conffiles will improve their lives somehow. Not really sure how to curb that, but not with bugs in apache.