the following should explain it all really.
http://paidcontent.org/2012/09/10/wh...ok-prices-now/
Agency pricing has been declared legal, and it doesn’t go away now. The settling publishers can still sell their ebooks to retailers under agency contracts, where they set a book’s list price and the pay the retailer a commission. The difference now is that retailers can discount the ebooks however they want.
However, there are limited exceptions: The settlement allows HarperCollins, Hachette and Simon & Schuster to negotiate new contracts that include “a commitment from an e-book retailer that a retailer’s
aggregate expenditure on discounts and promotions of the Settling Defendant’s ebooks will not exceed the retailer’s
aggregate commission under an agency agreement in which the publisher sets the ebook price and the retailer is compensated through a commission.” The settling publishers can also negotiate one-year contracts that “prevent e-book retailers from
cumulatively selling that Settling Defendant’s e-books at a loss over the period of the contract.”
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this prevent a retailer from taking a loss on an aggregate / overall basis of a publisher catalog. Which mean a retailer can take a loss on a particular book if they want to.
In fact, selling 10% of book titles at loss and selling 90% of book titles at profit is legal as long as the retailer don't make a loss on the overall catalog.