Today I had the same problem with parallax that after regenerating the DOM elements I could not call the $("#someID").parallax(). But I found the solution and I hope it will help you too. You need to reference an other script (not just the jquery-parallax.js):
<script src="script/vendor/parallax.js"></script>
After that in the javascript file where you play with the DOM. Call this every time after the manipulation:
var pDiv = $('#animations')[0]; //parallax works with DOM elements -> unwrap it from the jquery element
var p = new Parallax(pDiv); //recreate the parallax on the element
After this you don't need to call anything else. It worked for me. I hope it will be a good solution to you too.