In our production environment, our end users open PDFs through our application. They then edit the PDF and click "Save." Prior to Reader X, this would automatically save to the correct folder supplied by our application. Now, however, it always displays a "Save as" box and the user must choose where to save it. We can't have this at all as the file structure should be transparent to our users and we don't want them accidentally saving over another file or deleting one. What can I change in the settings to fix this?
Automatic (scripted) save to disk arbitrary locations are disallowed by Reader X for security reasons.
has the details.
If the environment is controlled, if you white list the folder that is being saved to, the prompt will longer be forced. Download the Application security guide from http://learn.adobe.com/wiki/display/security/Application+Security+Library and look at chapter 3.6.2