What's being said is that the Avast "Chest" (which is basically the quarantine) stores not only infected files (virus, trojan etc) but copies of certain system files.
Everything in the chest is protected. Nothing can interfere with it (except the user or the program), nothing can get in or out.
Avast stores copies of some system files in there, (generated by the VRDB, which you may see working beside the Avast icon when the computer is idle) so that good copies can be restored to the Windows System folder in the event the originals are damaged by an infection.
You will see there are different categories within the chest: Infected, User, System, and All.
One of the things being said above is that perhaps "system" files shouldn't be normally accessible or visible to users, as it can confuse.
So the only thing you should be alert to is "infected files".
All clear?
Now. We need to know more about the warning that was popped up. If you can remember anything about the alert, that would be good. If it happens again, write down all the details (or take a screenshot if you can) and post it.