With Bootstrap, we do a lot of "binding" of html elements, with javascript, e.g. tooltips or popup previews for image files. This is done by calling a JS function bind_bsui_components when we ready the document.
With Primefaces, we do a lot of ajax calls that update parts of pages - when that happens the bootstrap binding is lost. This is because the update replaces the html, but doesn't know to call the rebinding.
We currently solve this by calling the javascript for each update with oncomplete="bind_bsui_components"
This is prone to error, because we have to remember to put it everywhere.