The /var/cache/apt/archive directory is meant to be temporary storage. apt-get and other package installers have a command called "clean" which deletes the contents of this directory to save space. If the packages have disappeared from this directory you probably are not getting them back.
I am not sure why you want to keep the files around unless you are installing multiple systems. For a single system you typically do not need the .deb files once they have been installed; to upgrade packages you have to download the entire upgraded package again.
If you are installing Debian on multiple machines then there are some tools that can cache your .deb files more permanently. The most useful one I have found is "apt-proxy", which transparently creates a partial mirror in some directory you create. Unfortunately apt-proxy is in a state of transition now, and if you want it you should visit http://apt-proxy.sourceforge.net
to get a copy. (You want version 1; version 2 is very buggy.)
The apt-proxy page has a list of alternative tools as well. The only other one I have used is "apt-move", which is a package that does exist in the official Debian archives. Making mirrors with this package requires more manual intervention, however.