Just curious to know if a fixed layout ePub and a free flowing ePub, of the same title and contents, would have to have their own ISBNs based on the different structure type or can a single ISBN be used for both file types? Some retailers do not want fixed layout ePubs so a free flowing ePub was created.
Yes, you should. The point of ISBNs is to identify distinct formats--in the world of print, a paperback and a hardcover would have different ISBNs. As Bowker (the US ISBN authority) says on their site:
The ISBN identifies a specific title, edition, and format being made available for sale. You will need an ISBN for each unique version of your book. For example, if you plan to release a hardback edition, softbound edition, EPUB edition, MOBI edition, and PDF edition, then you will have 5 unique versions of your book.
One of the most important things that an ISBN will do for an ebook is ensure that the right version gets sold to people with the right devices, so that nobody ends up with a format that they can't use. Because fixed layout is not something that all reading systems support, you'll want a different ISBN for fixed layout than for reflowable.