I have made a very similar experience, downloading and installing many
packages and I thought they were save in the archives directory. After a
while I  have discovered that many had disappeared, although Synaptic
was set to keep the packages. I thought at first, that maybe ATPonCD had
erased them but, after Mario Splivalo's bug report I checked more
alertly and it really seems to be the update manager. Only the number of
packages can be checked (as they are many) and directly after update
obviously the number had increased but, after a restart suddenly they
had decreased again. So it is quite unclear what is happening in that
directory, under which rules is it administrated and which processes do
have an impact on what it is in and what not.

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https://bugs.launchpad.net/bugs/581014

Title:
  /var/cache/apt/archives contents gets deleted even when Synaptic is
  told not to do so

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