Changes to HTML are not saved because HTML is not part of the data included in any web form submissions; this is true for any web forms, not just LF, and it makes a lot of sense when you consider that a client-side browser can manipulate the HTML however the user wants, so accepting those changes could cause a lot issues and even create security vulnerabilities.

If you want those changes to be reflected in the form saved to the repository, then you'll need to write a version of your code that can run on the read-only copy. Your scripts will still be triggered when the Save to Repository task runs, but the content of the form will be different.

For example, all of the input elements are converted into static content in div elements just like when you have a read only user task, so you'll need alternate code that can produce the same results from a read-only version.

Another option to investigate, if it is possible for your scenario, is to add pre-defined custom html elements to the form and use field rules to show/hide them based on the user selections because those rules will be applied in Save to Repository without any extra code.