I highly recommend you read Andrew's post and then come back here, but if you don't have the time, I'll provide a quick run-down and some commentary.
As I've noted before, books are sold from publishers to accounts by the publishers' sales reps (sometimes called "account managers") and are bought by the accounts' buyers during what are termed "sales calls." The ultimate outcome of a sales call is a list of numbers: the number of copies of each book presented that the buyer would like to take for the account.
For national accounts like Borders or Barnes & Noble, sometimes that number is pretty good, say 1,000 - 2,000. Sometimes it's very good, say, 3,500 - 6,000. And sometimes it's just super, say, 10,000+.
And sometimes, alas, that number is: 0.
Yes, zero is an option, and when a buyer decides not to take any copies of a given title, that title is said to have been "skipped." (Noun: "a skip," as in, "Venezuelan Vampire Vixens V was a skip due to poor sales of Venezuelan Vampire Vixens IV.") There are those pesky comps again. More on those in a future post.
What does it mean for you if a national chain skips your book? Well, to be flat-out honest, you are somewhat doomed. A lack of presence in the national chains is a severe handicap, and your sales will then essentially be limited to the independents and the major on-line retailers, such as Amazon. (Yes, there's also the "mass merch" channel—e.g. Sam's Club, Costco, Target—but they take far fewer titles than the chains. If you get skipped at B&N, you're sure as hell not going to be shelved at Wal-Mart.)
You are only somewhat doomed, however, for the following reasons: because Amazon has the ability to reach consumers anywhere, 24/7, if your book sales really take off there, you certainly won't be skipped again when it comes time for the national accounts to buy your next book. (You'll also make some handsome royalties. Ka-ching!) Then again, if you languish at the bottom of Amazon's search results, you won't get those sales and may never be heard from again. On the other hand, word-of-mouth at the independents might score you mainstream reviews and increase your sales, but that's a pretty big "might"—the independents can only do so much. (As Andrew notes, the number of independent book stores has dwindled from 7,500 to just 1,700 over the past two decades.)
You're right to be angry, sad, depressed, confused, or all of the above if your book gets skipped by one of (or more than one of) the national chains. But what can you do about it?
• Don't give up. No one is more interested in promoting you than you are. Ask your agent and editor what you can do to help sell yourself and your book. Now might be the time to change your mind and actually go on that six-city book tour, or even just accept an offer to appear on a local radio show.
• Visit your local independent book store(s). Try and get them to buy a few copies of your book. If they say yes, ask if you can do an author event or sign some stock. Oh, yeah, and continue to shop at said stores so they don't go out of business.
• Take your fight to the blogosphere. If you've got a web site or a blog—and you should—try to get the word out through that outlet. Let your friends know on Facebook. Tweet about it. (Just don't say anything in anger, or something you might regret later.)