Should I delete my save file or restart in Undertale?

After I've realized that killing Papyrus did have some major consequences, I decided to spare 0 mercy on the king wishing to go for the asshole route, and after "defeating" Flowey and sparing the king on a reload, I was greeted by a punishment by said flower.

I did a save reset to make a more pacifist run (do I get any difference if I kill zero enemies, or is that too hard of a challenge?), but contrary to the first run, I didn't encounter with Flowey after falling into the Ruins. Does this mean that my save is still corrupted by Flowey?