I think the best you can do is delete that one file from your server drive. It happens very little 
That one file? I get several... and from cron everyday....
> /etc/cron.daily/check_store:
>
> check error - probably no last-modified header
>
http://w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB893066-x86-DAN.psf> /opt/windows/cache/store/w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB893066-x86-DAN.psf
>
> HTTP/1.1 200 OK
> Connection: close
> Date: Fri, 27 May 2005 02:05:40 GMT
> Server: Microsoft-IIS/6.0
> X-Powered-By: ASP.NET
> Content-Type: application/octet-stream
> Content-Length: 1315566
> Accept-Ranges: bytes
>
>
> check error - probably no last-modified header
>
http://w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB893086-x86-DAN.psf> /opt/windows/cache/store/w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB893086-x86-DAN.psf
>
> HTTP/1.1 200 OK
> Connection: close
> Date: Fri, 27 May 2005 02:05:41 GMT
> Server: Microsoft-IIS/6.0
> X-Powered-By: ASP.NET
> Content-Type: application/octet-stream
> Content-Length: 2464494
> Accept-Ranges: bytes
>
>
> check error - probably no last-modified header
>
http://w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB890859-x86-DAN.psf> /opt/windows/cache/store/w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB890859-x86-DAN.psf
>
> HTTP/1.1 200 OK
> Connection: close
> Date: Fri, 27 May 2005 02:02:16 GMT
> Server: Microsoft-IIS/6.0
> X-Powered-By: ASP.NET
> Content-Type: application/octet-stream
> Content-Length: 41291502
> Accept-Ranges: bytes
>
>
> check error - probably no last-modified header
>
http://w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB885835-x86-DAN.psf> /opt/windows/cache/store/w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB885835-x86-DAN.psf
>
> HTTP/1.1 200 OK
> Connection: close
> Date: Fri, 27 May 2005 02:02:16 GMT
> Server: Microsoft-IIS/6.0
> X-Powered-By: ASP.NET
> Content-Type: application/octet-stream
> Content-Length: 42545900
> Accept-Ranges: bytes
>
>
> check error - probably no last-modified header
>
http://w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB885250-x86-DAN.psf> /opt/windows/cache/store/w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB885250-x86-DAN.psf
>
> HTTP/1.1 200 OK
> Connection: close
> Date: Fri, 27 May 2005 02:05:42 GMT
> Server: Microsoft-IIS/6.0
> X-Powered-By: ASP.NET
> Content-Type: application/octet-stream
> Content-Length: 1011436
> Accept-Ranges: bytes
>
>
> check error - probably no last-modified header
>
http://w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB873333-x86-DAN.psf> /opt/windows/cache/store/w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB873333-x86-DAN.psf
>
> HTTP/1.1 200 OK
> Connection: close
> Date: Fri, 27 May 2005 02:02:17 GMT
> Server: Microsoft-IIS/6.0
> X-Powered-By: ASP.NET
> Content-Type: application/octet-stream
> Content-Length: 6206188
> Accept-Ranges: bytes
>
>
> check error - probably no last-modified header
>
http://w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB873339-x86-DAN.psf> /opt/windows/cache/store/w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB873339-x86-DAN.psf
>
> HTTP/1.1 200 OK
> Connection: close
> Date: Fri, 27 May 2005 02:05:43 GMT
> Server: Microsoft-IIS/6.0
> X-Powered-By: ASP.NET
> Content-Type: application/octet-stream
> Content-Length: 305388
> Accept-Ranges: bytes
>
>
> check error - probably no last-modified header
>
http://w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB890175-x86-DAN.psf> /opt/windows/cache/store/w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB890175-x86-DAN.psf
>
> HTTP/1.1 200 OK
> Connection: close
> Date: Fri, 27 May 2005 02:02:18 GMT
> Server: Microsoft-IIS/6.0
> X-Powered-By: ASP.NET
> Content-Type: application/octet-stream
> Content-Length: 1043180
> Accept-Ranges: bytes
>
>
> check error - probably no last-modified header
>
http://w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB894320-x86-DAN.psf> /opt/windows/cache/store/w2ksp5.windowsupdate.microsoft.com/isapi/pstream3.dll/w2k/Windows2000-KB894320-x86-DAN.psf
>
> HTTP/1.1 200 OK
> Connection: close
> Date: Fri, 27 May 2005 02:05:44 GMT
> Server: Microsoft-IIS/6.0
> X-Powered-By: ASP.NET
> Content-Type: application/octet-stream
> Content-Length: 708846
> Accept-Ranges: bytes
>
>