I'm not a package maintainer, but isn't this just the sort of thing
that dpkg-divert is for?

  Tiger (at least the Debian package version), for example, is
"dpkg-divert aware" when it goes around checking md5sums, so even if a
file has been dpkg-diverted the checksum test is still able to verify
whether you still at least have a valid copy of the original package file.

-Zach


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