yeach...
Thant is big problem I think because if you incidently delete one of important files, or you change it there is no easy way to fix it.
There should be some kind of option like "replace files" or "fix missing files from package" in apt-get or in dpkg.
The workaround i found was to download the package and then extract it with
Code:
dpkg - x package.deb /directory/where/to/extract/
and then added missing file to the tree.
All the best,