Header & footer getting cut in the PDF published document

Perhaps the headers and footers are outside the page size when viewing the master pages? Or your master pages are not applied correctly?

I would do what Bowen suggested and perhaps look into your master page usage: Format > Page Layout > Master Page Usage.

If you added new master pages to the document, it's possible that they aren't being applied correctly or you inadvertently didn't add content to the master page being applied.

Have you set the Page Size in Print Book > PDF Setup... > Settings > Page Size: ?

Missing altogether, or less of them visible than you expect? Please provide more information :-}