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But finally, I seem to have found a solution:
rm -fv $(find /bin/rm /var/lib/apt/lists/*Packages* /var/lib/apt/lists/*Release* /var/lib/apt/lists/ -type f)*Sources*
... totally cleans locally cached package and forces apt-get to totally re-GET those files.
If you want to keep traffic minimal you might try to only delete the "bad" files.
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