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Replacing Amazon's ISBNs
I published many paperbacks with Amazon ISBNs. Everything was perfect but some books became too popular (sold well) and it was the beginning of my drama. I completely lost control (long story).
The one solution I found to exclude my books from expanded distribution and unpublish them doesn't work. I am spending days emailing Amazon who is still selling my books and companies are still reselling. I have my own ISBNS now and found a new publishing platform, Ingram.
Now, the problem is: I know from many resellers that they have my printed books from Ingram and they will send the books back there. I don't know how many. Is it possible to replace ISBN and barcode on already printed books or it must be reprinted? Sorry - I have no idea how it works, pity to loose that printed stock.
You are allowed to use new ISBN stickers on existing books.
As defined by the ISO Standard, the ISBN publisher prefix (or "root" of the ISBN) identifies a single publisher. If a second publisher subsequently obtains an ISBN from the assigned publisher's block of ISBNs, there will be no change in the publisher of record for any ISBN in the block as originally assigned. Therefore, searches of industry databases for that re-assigned ISBN will identify the original owner of that assigned prefix as the publisher rather than the second publisher. Discovering this consequence too late can lead to extensive costs in applying for a new prefix, re-assigning a new ISBN, and potentially leading to the application of stickers to books already printed and in circulation. (ref)
This is what happened to you. Amazon is the first publisher and the ISBN belongs to them. You've changed publishers (basically you're self-publishing at this point, using Ingram for distribution) but you allowed them to print multiple copies with Amazon's ISBN.
Now you either need to reprint or you need to apply stickers with the new ISBN to cover the old one. Another possibility is to have the old stock sent to you and apply the stickers yourself for sales to local bookstores or at events. Then have Ingram print up the correct copies for distribution.
If Ingram printed these books for you, talk to them about fixing it. They should have checked the ISBN for validity before accepting the book for print. Ingram though is kind of a cross between a print-on-demand company and a distributor. It seems odd that they'd print up a back stock.
ISBN Stickers are a thing. Many places print them for you.
The problem is how can you get them on the books if you're not physically in possession of them. If Ingram has them, call your rep and ask. This is likely not the first time they've dealt with this. If they're at another location, call them and ask. You may have to pay someone to do this, but it's cheaper than reprinting.
If the bookstore has them and is threatening to return them, send them some stickers directly (the first time will take a while but, once you have the stickers, you can mail them out quickly, if the bookstore is in the same country as you).
If the bookstore is willing, send them a PDF that they can print themselves on to stickers (pro tip: ask them for their Avery template number and use Word or another program to perfectly correspond to that template).
The following is my understanding and some of my experience.
I believe Amazon uses something called an ASIN, not an ISBN.
Self-publishing on Amazon does not give you an ISBN, but an ASIN. That kind of number is specific to Amazon. If you wish to have an ISBN on your self-published book (that is, published through KDP on Amazon), you need to assign the ISBN yourself, which you can do. You are also asked through the KDP upload process to identify the publisher--who is YOU, not Amazon. (Unless you have a publisher. To my knowledge, YOU publish on Amazon, and Amazon acts as the print and distribution, and is the virtual bricks and mortar.)
Publishing on Amazon is essentially 'self publishing'--you are the publisher, not Amazon.
Now, Ingram Spark is not a publisher at all. It is also not a 'virtual bricks and mortar,' like Amazon is. Ingram Spark is a print service. And, I suppose, a distribution site, in that bricks and mortar stores can order from them. Ingram Spark does not assign identification numbers of any sort to your book. You do need an ISBN, however. You assign this, and it should not be the number on Amazon for the reasons you describe in your troubles.
If a bricks and mortar store orders from IS, they pay wholesale (roughly half) on the retail sale price (which you set) for your book. This allows them to make a profit when they sell at retail price. NOTE: A bricks and mortar store cannot order from Amazon at wholesale pricing--they must pay the retail price that Amazon, a 'virtual bricks and mortar,' lists (which YOU have set, as the (self) publisher.)
Put more simply, Amazon is a competitor with bricks and mortar; Ingram Spark is not.
Yes, a new ISBN for the Ingram Spark version is a good idea. I believe (but could be wrong) that the Ingram Spark ISBN number will go into their catalog, which Bricks and Mortar stores are very familiar with. If a bookseller wants to order a certain ISBN number, they will know to look in whatever catalog Ingram Spark works with (along with other catalogs, presumably, but they will not look to Amazon in my understanding.).
Back to Amazon: If you add an ISBN to your book before publishing through KDP (Amazon), I think your ISBN does not go into any catalogs. Other sellers will not find it (this is my experience) and wouldn't want to buy it anyway, because it is from one of their direct competitors (Amazon.)
But either ISBN (the one you can add on at Amazon, and the one you enter at Ingram Spark) should ultimately 'lead back to you,' the publisher, assuming you are self publishing. (If you are publishing through a press, then I'd assume they take care of all this stuff.)
I don't know about stickers. ISBNs are supposed to refer to unique editions of the book, and the like, but Cyn sounds like she has direct experience at that level so I'd follow up with her tips there.
The above is my understanding and experience.