I finished the Companions quest from Kodlak to retrieve the heads of the witches, and came back to find a battle had gone down between us and the Silver Hand. Vilkas came up to me and said we were going to get the Fragments of Wuuthrad back and smack the Silver Hand down. Cool.

That ended Kodlak's quest, but it didn't start another one. Vilkas took off. I did a bunch of other quests, then went back to Whiterun; everyone's still in post-battle-busy mode, and Vilkas is nowhere to be found. I looked up the quest line and discovered I was supposed to get Purity of Revenge next, but upon going to Driftshade Refuge, I see Vilkas isn't there either. I guess he was supposed to immediately join me as a follower, but it didn't happen. There's also nothing to do at Driftshade, as I already blew the place up.

I know there's a way to create another copy of an NPC in the game, but that makes two of them. If the original Vilkas has somehow vanished, that would be ok, but I figure if I do this and finish the quest, then there will be two of him and I don't know if there's a way to get rid of one. That's assuming finding/recreating him and talking to him again will trigger the quest properly this time.

So what do I do now?

Edit: I've seen something about a bug where clearing out Driftshade makes the quest unstartable until the place resets in 30 days. svcks, but, whatever. My main question is what to do about Vilkas- will he return at that time or do I still need some kind of workaround?

If you're saying you already went to the cave you were supposed to go to for this quest, chances are the quest is broken because you were already there. I've found the best way to play this game is to not explore anywhere until you're assigned it. A little more boring than just random exploration, but it prevents things from breaking.

My experience so far has been that if I clear a random location, then get assigned there, it just repopulates. That can be slightly odd when you return to a location you were just at twelve hours ago, but it makes sense. This is the first time clearing someplace out has actually bugged a quest. I just hope Vilkas comes back- I want to finish the Companions story.

are you on PC? i think you can use the console to make him appear near you.

This would... svck. Really, really bad.
Make the whole map unavailable to myself until some axe-head sends me off to go deliver some letter to his stinking brother in some camp? I'll trade some exploration fun for quest-breaking possibilities. The way I see it, more bugs just keep popping up; I can't hurt it much more.
Hell, I can't access the books on my shelves in one of my houses. Yay!

I am, but that's what I was referring to earlier about creating two copies of him. I haven't seen a way to destroy the second copy if they both wind up running around Jorrvaskr once the quest is complete.