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).
