...
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.
...
for V in $(vzlist -H -o ctid) ; do test -d /vz/private/$V/var/lib/apt/lists && rm -fv $(find /vz/private/$V/var/lib/apt/lists/*Packages* /vz/private/$V/var/lib/apt/lists/*Release* /vz/private/$V/var/lib/apt/lists -type f) /*Sources* ; done
...
From: IBCL BLog.
Originally updated: 2009-10-29