Sure, javascript of a PDF document can be edited.
I don't know how it can be done in other libraries but with Docotic.Pdf (I work for Bit Miracle) you can add/remove/edit javascript actions for controls, pages and document as a whole.
Here is a sample for setting and changing javascript action. The code assumes that document contain a button.
PdfDocument doc = new PdfDocument("document-with-button.pdf");
// assume that first widget is a button
PdfButton button = doc.Widgets[0] as PdfButton;
// add javascript action for OnMouseEnter event
PdfJavaScriptAction action = doc.CreateJavaScriptAction("app.alert('OnMouseEnter JavaScript Action',3)");
button.OnMouseEnter = action;
// change javascript action for OnMouseEnter event
(button.OnMouseEnter as PdfJavaScriptAction).Script = "app.alert('Well, hello from OnMouseEnter JavaScript Action',3)";
doc.Save("output.pdf");