Hi Jeffrey.
First, in general, we don't recommend using old Helix versions. You should update everywhere to 2.1.3.
Second, I think more robust method for Custom CSS is using custom.css file, also becuase it's easier to find mistakes, like missing "}" etc. Please copy/cut and paste all the CSS you want to use into the newly created file, and you’ll find that Webmaster Live becomes much less problematic.
About header gone, it can be caused by: old template version, becuase some months ago Joomla 5 changed one thing and that caused problems with template options.xml file. Were many topics on forum about that. Or problem with broken custom CSS code (less possible).
And you forgot to tell us, what template name you're using? Raw Helix Ultimate or template based on that framework. I only remind you, that we can help here only if you have template directly from Us, not external seller/developer (Support Policy 8.8).