Adobe Reader X runs in protected mode.
"Do plug-ins have read and write permissions to things like config files that maybe stored on the user's system?
Plug-ins will not be able to write log files to non-whitelisted locations. They can continue to write logs to the Temp directory (as returned by GetTempPath() Windows API or equivalent Acrobat API). Another white-listed location is Adobe Reader's own appdata area."
You can write out silently only to the whitelisted locations. The other alternative is to throw a save as dialog for user to select the location and save.
Is it possible to add a folder to the Whitelist with all subfolders dynamicly?
No, not dynamically. If you could do it dynamically, so could any sort of exploit or malicious document.
See http://forums.adobe.com/thread/755518?tstart=0 for steps on how to do it as an administrator for a specific folder.