The patch routine is supposed to do a dry run, test to see if there are any errors, produce a report that outlines where it's failing and then exit without touching any files.
If any one line item in the list fails to patch, the whole patch is supposed to exit, leaving all the files intact and unmodified.
Always do a full backup of your Magento application and database before applying the patch as other issues can crop up.
People are having issues with the patch applying correctly, but not having the database installers run for creating the tables for variable/block permissions. This is probably happening because they aren't disabling the compiler and Magento cache before installing the patch
