The following does not solve the problem, but limits the frequency of the 
problems when using squid as a proxy. I added the following two lines to the 
squid configuration:
---
acl DEBIAN_NOCACHE urlpath_regex Release Packages.bz2 Translation.*.bz2 
cache deny DEBIAN_NOCACHE
---

This prevents the files that change frequently from being cached by
squid. As they are relatively small, the impact on the bandwidth use is
not that bad.

It does not solve the problem with mirrors being temporarily out of sync
or the race condition in file access.

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

Title:
  apt repository disk format has race conditions

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