Doesn't this do what you need?

http://www.unix-ag.uni-kl.de/~bloch/acng/html/maint.html#cleanup :



  Validate by file name AND file contents (through checksum)  Checking file 
contents where possible, also attempt to detect incorrect file size information 
in the cached metadata. Note: the check results are stored only once, future 
calls without this option can overwrite the results again. Use action buttons 
(see below) to delete corrupted files after the scan.  Force the download of 
index files  Sometimes it may be needed to redownload all index files, 
explicitly replacing the cached versions. This flag enables this behaviour.  
Purge unreferenced files after scan  Avoid the use of the orphan list and 
delete files instead. This option is dangerous and should not be used unless 
when absolutely no mistakes/problems can happen. Instead, it's possible to view 
the orphan list later and delete then (see below).Regards,
Eduard.

 
 
  ----- Ursprüngliche Nachricht -----
  Von: Konrad Zimmermann
  Gesendet: 11.10.11 08:46 Uhr
  An: Debian Bug Tracking System
  Betreff: Bug#644959: apt-cacher-ng: corrupted files linger in cache
 
   
Package: apt-cacher-ng
Version: 0.6.7-1
Severity: important

>From time to time apt-cacher-ng downloads corrupted files either
because the version on the server is or because it gets garbled
during transmission. These files then stay in the cache and apt
(or aptitiude in my case) complains about wrong hash sums on upgrades.
After manually deleting the file from cache, apt-cacher-ng reloads it
and upgrades can proceed.



-- System Information:
Debian Release: wheezy/sid
 APT prefers testing
 APT policy: (990, 'testing'), (500, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.0.1-01 (SMP w/4 CPU cores; PREEMPT)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages apt-cacher-ng depends on:
ii adduser 3.113 
ii debconf [debconf-2.0] 1.5.40 
ii libbz2-1.0 1.0.5-7 
ii libc6 2.13-21 
ii libgcc1 1:4.6.1-4 
ii liblzma2 5.1.1alpha+20110809-2
ii libstdc++6 4.6.1-4 
ii zlib1g 1:1.2.3.4.dfsg-3 

Versions of packages apt-cacher-ng recommends:
ii ed 1.5-3 
ii perl 5.12.4-4

Versions of packages apt-cacher-ng suggests:
ii doc-base <none> 
ii libfuse2 2.8.6-1

-- Configuration Files:
/etc/apt-cacher-ng/security.conf [Errno 13] Keine Berechtigung: 
u'/etc/apt-cacher-ng/security.conf'

-- debconf information:
 apt-cacher-ng/gentargetmode: No automated setup   



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