Pagination and master pages
PDF ebooks have pages like print. But reflowable formats, like epub, have no fixed pages as such. So there is no pagination. When you export an InDesign file to epub, it will pretty much ignore:
- running headers/footers and page numbers on master pages, and
- margins or page size.
So don’t put any important content on a master page.
Also, if you have to override master page items on your pages, but you don’t want them in your epub, here is some useful advice on a workaround in CS4.