To give a little more detail, when you press the submit button, the form submits its data to the server (only includes fields that are linked to a variable from the Form Layout page, so basically only the Laserfiche drag-and-drop fields), which Forms then stores in the database. When the process hits a "save to repository" step, Forms reloads that submission by browsing to a particular URL, and uses a 3rd party tool called wkhtmltopdf to convert that rendered page into a PDF document. This means that any Javascript-based events that change the appearance of the form will only be rendered if they are designed to run when the form loads... not if they are in response to user-driven events.

I have seen some users create hidden Laserfiche fields to store status variables, and then create some javascript functions that look at the status on loading and recreate the proper changes to the form based on those values. In this case, you can get the changes rendered into the PDF, but only if the code runs without user interaction and when the form loads.