Had a similar situation with a new site I'm working on (slideshow above affixed navbar changes height when window resizes, leaving the affixed navbar with the wrong offset).
The answer is to delete the affix data from the jQuery data cache and then remove any classes associated with the affix plugin, like this:
$([selector]).removeData('affix').removeClass('affix affix-top affix-bottom');
I found that at the bottom of https://github.com/twbs/bootstrap/issues/5870