(spoiler warning. Based off of the second S9 trailer, and an upcoming episode)
I think it’s going to be the Legion of Doom’s fault the Windigos come back.
There’s three of them if you don’t count Grogar, there’s presumably three Windigos again, there’s three pony races, Chrysalis commented on Discord “really being something before friendship ruined him,” and there’s also the line of hers that The Summer Sun Setback ended on. I’m not actually seeing how Grogar factors into the main problem, if he does, other than him possibly being incapacitated first thing.
One possibility those three have (or two of them, or one, depends on what happens) is they decide to stop fighting the heroes so the Windigos won’t ice up everything, up to and including themselves. If Chrysalis was so self-destructive she couldn’t even stop for that, wouldn’t surprise me.