ISBNs Best Practices
We recommend that you use the same ISBN for your MOBI, EPUB, and PDF versions of files; however, you should use a unique ISBN for any variants across one of those core file types. For example: An EPUB with audio should have a different ISBN than an EPUB without audio. A fixed format EPUB should have a different ISBN than a reflowable EPUB.
If you have retailer-specific files under the same ISBN, please remember that if you need the file to be updated, you must send an update per retailer-specific file. ie, an update to your 'generic' epub, will not update your epub that is specific to B&N.
New editions of an eBook require a new ISBN. A title is considered a new edition when over 20% of the content has been changed. iBooks allows version information to be embedded in EPUB 3.0 files using the ibooks:version tag. See the section Book versioning in EPUB 3.0 and special note re: iBooks here: Retailer Quick Guide
From The International Standard Book Number System ISBN Users' Manual (link to full publication available through BISG resources page link below):
If the on-demand version of a publication is in a different product form from the previously published non-on-demand version, (e.g. if a hardback becomes a paperback when it shifts to being on-demand), a new ISBN is required, just as for any other changes of product form. Minor changes to trim sizes in order to comply with the specifications of on-demand printing machines do not require a new ISBN.
For full explanations of industry use of identifiers, review these guides: