you could add a query string parameter to your links pointing to other parts of the book so that instead of
<a href="page5.html">reference to page 5</a>
you would have
<a href="page5.html?reference=ref1">reference to page 5</a>
and on page5.html you can highlight the reference with a span tag
Lorem ipsum dolor sit amet, <span id="ref1">consectetur adipiscing elit</span>.
and add script similar to this
var refToHighlight = getQueryString("reference"); //you will have to write your own function to get qs data
//removes the span and replaces it with a link
$('#' + refToHighlight).replace('<a class="reference" href="#"/>');
//changes the link back to span when clicked
$('.reference').click(function(){
$(this).contents().replace('<span/>');
});
This way when a user browses regularly to page5 (clicking links not ending in ?reference=ref1) the reference will not be highlighted as its marked with a span, but on the other hand if the user clicks a link containing the query parameter the span will be changed to a link that will highlight the reference now.