Unsure. You can test it. iBooks may store highlights and annotations by CFI:
http://www.idpf.org/epub/linking/cfi...ec-epubcfi-def
In testing, there seems to be some leeway. I can rename files and the highlights remain. Additional paragraphs later in an HTML file won't affect highlights made earlier. I can also change DOM elements such as changing a p to a div, and for example, if a highlight is in the 5th paragraph at some position if I change the p to a div, highlights remain. If a fix a typo and character position changes, or I add or remove some element like an italic, anchor, etc., position will slightly shift.