Hi Aditi,
It sounds like there may be a rule issue going on but I don't know for sure. Would you be able to provide the rule logic you used when hiding the fields and the rules you used on the PDF Control? Maybe that will help us in helping you better.
Is this along the lines of the rules you set up?
Events: When your PDF Control is Clicked
Actions: Hide a Form control
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Another option is to 'uncheck' the Enabled options for the controls you want to be hidden in the Properties > General pane and then instead set up rules to Hide the Form Control and then later have a rule to Enable the control when you need it.
I have controls hidden on radio button selection. IF use selects a perticular value I hide some perticular controls or show some. In this case when I generate pdf on submit button click when controls are already hidden, the pdf has both hidden and visible controls.