Board Thread:General Discussion/@comment-32784606-20170805013431/@comment-29933267-20170805194144

At some point, Papyrus greets us before we enter Alphys' lab to be confronted by the amalgamates, by saying, "HOWDY!"

And at the end of the Pacifist route, he expresses knowledge of a 'tiny flower' before our fight with Asriel.

So I would think that he knows Flowey, also hinted at by Sans, but then thought to just be an Echo Flower. As we know, Flowey used to have the power to SAVE. If Papyrus has spoken to Flowey mutliple times, then it is likely that he too, knows about the SAVE files.