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How do I make it remove the .par downloads after the main downloads are complete? I am very frequently being left with those in the list not doing anything...just left over. Thanks.

What version are you using?

In the latest, it removes the pars when all the files that make up the set are confirmed and repaired. If you never download all the files, it won't remove the pars because it's waiting for more files. Older versions might not have cleaned up as well. You can see the par counts. They should tell you how much of the set has downloaded.