In the meantime - as it is fairly obvious that this will not be done
instantly and unlikely to be in time for q-freezes - you might want to
explore solutions similar to bittorrent which are available today with
apt-p2p or apt-transport-debtorrent (as these are by definition hash
based) or setup a service like http.debian.net which in your case would
only redirect to fully updated mirrors -- which might even speeds up
your updates on the machine if it redirects the same client to different
mirrors (to improve this further you might like to backport deb#668111
for apt).

Either doesn't solve all problems, but should be able to fix at least a
few for now.

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https://bugs.launchpad.net/bugs/972077

Title:
  apt repository disk format has race conditions

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