When an appeal case is won, they reset the clock on processing your application. It's unfair, but it means that it sits in queue until someone gets around to looking at it again. Since they've already asked you for more documents (which is actually pretty fast) you should expect someone to look at it 1-2 months after the deadline they gave you - so if they said "you must submit a response by august 29" then you would expect to hear back from them in October. But if the deadline was September 30, you probably won't hear anything until November or December.
They probably are done with background checks, though they may need to update them if you have been living outside Canada.