Run JavaScript before flattening in Output

I have some forms that I sometimes need to flatten with Output before emailing to a user, sometimes not. On these forms I have some JavaScript that decides if certain fields are visible or not depending on certain data in the forms. This JS works fine when I render the form unflattened (i.e. not using Output). When I flatten the form with Output, my JavaScript doesn't run and the fields are unaffected. Is there any way around this? I would love to find a way to do this on the PDF rather than get in to some custom server side code in my PHP.
- Nathan

So here's some additional information. I was able to get this code to work on the server:
Ultra_Form.Page1.Buttons.SaveAndClose.presence = "visible";
But the code below will not run correctly on the server (although it will run on a non-flattened form on the client):
Ultra_Form.Page2.presence = "visible";
Ultra_Form.Page2.TF1.presence = "visible";
Essnetially what I'm wanting to do is show a page that is set to "Hidden (Exclude from Layout)". Works on the client, but not on the server so far.
Any ideas?
- Nathan

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