Okay, I did that and it solved the problem. Now I have a new page without the custom JS code.
I really hope this is not your vision of the future! Please don't make us do this after every update. As I said before, I think the one page navigation should just work out of the box or, even better, there should be an (actually working) part in Cornerstone where you can choose a specific menu to act as a one page navigation with options to set the animations and margins/offsets.
Also, I just compared the code @Nabeel gave me earlier in this thread with the old code I had on my /juniors/ page and quickly realized that it was the exact same code! Since the one page navigation worked before the update, this proves that the problem was not a wrong custom JS code but rather some other bug caused by this update.
It was also most certainly not a caching problem. Despite my earlier hesitation I completely uninstalled W3TC yesterday, put Cloudflare in development mode, and cleared all the caches. And yet, I was still not able to remove the custom JS.
I'm not a professional developer by any means but I would like to think of myself to be somewhat advanced in using Wordpress and the X/PRO theme. I like the direction you are developing your theme, that you are making it more flexible for advanced users, and that you don't rely on pre-designed elements so much anymore but rather give us room for our own creativity with your framework.
Please keep in mind, however, that X/PRO probably has a steeper learning curve today compared to other premium themes. When I think about how much time I spend with your product to tweak, optimize and debug it, I can only imagine how overwhelmed and frustrated less advanced users must be.
Credentials to my site are attached in a secure note in case you want to have a look at it.