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Is there any way to autofill your Wishlist and Tradelist values, since the TCG Browser site knows how many of each card you should have?
Yes, there is. On the wishlist tab click the Generate Wishlist button (2nd from left on top right). That should generate your wishlist, assuming you want 4 of each card. You have an option there to update it on collection sync, so you won't need to worry about that anymore. Similar for tradelist.