I recently removed Windows, and changed my dual boot system to Debian 32-bit and Debian 64-bit. Since the 32-bit is a new install, I have had several opportunities to upgrade the kernel (from Debian repos). As a final step in the installation of a new kernel, the /boot/grub/menu.lst file is rewritten.

It always drops the bottom part of the file where the Grub instructions for the 64-bit system are. It hasn't been a problem because I just go to the backup, menu.lst~ and copy those instructions back in.

Did I, perhaps, edit something out of that file that would encourage aptitude to save that section?

I'm pretty sure that this is called something like Automagic kernel list, and the configuration is part of the grub file. It doesn't exist on the machine I'm on now (gentoo), but it is in Debian and Ubuntu. There is a line in menu.lst that says
Begin Automagic kernel list here
or something like that,
then a corresponding line sometime afterwards. I'm sure it tells you where you should put stuff so that it doesn't get toasted on the next 'magical' update.

You can definitely put stuff before the automagically generated list, and that won't get touched. Perhaps not after.

It is kind-of configurable but I've usually given up, deleted the whole automagic section and just added the new kernels manually.