When I run chkrootkit on my server, it returns lots of .packlist files. From doing some research, it seems that 99% of the time these are false-positives and I don't need to worry about it. However, it creates a huge list in the chkrootkit output and I'm worried that I'll just skim over it and miss something important.

So, what is the purpose of the .packlist file? I opened a few and they seem to be lists of files, so logically it would be the list of files included in a package. I can see how that might be useful. Do I need to keep it around? Is it safe to delete it?

You need them...

But if you want an experiment - change the name of one
cp sample.packlist sample.packlist.test

then try apt get upgrade on a package in the list.

I use Yum to update this server, not apt-get. Does that make a difference?

hmmm... here's me thinking these were like the files apt creates to keeptrack of dependancies et al. Now I use yum all the time, lets see...

... anything like these ones?
Anyway - they still look needed. Experiment will be difficult without knowing the context - like these involve perl.