Folder handling
Sync empty folders will affect folders without content or whose entire contents have been filtered out.
Expand subfolders when loading session opens all folders automatically when a comparison is loaded.
Sync within archives treats archive files like regular folders.
File handling
Delete to recycle bin if possible
Moves files and folders stored on a local drive to the recycle bin instead of permanently deleting them. This option is ignored for deletions from network drives, remote services and within archive files.
Touch local files when copying to an FTP site
Many FTP sites do not allow Beyond Compare to control file timestamps, so when a file is copied to the FTP site, its date will not match the local copy. This option changes the local file timestamp to match the FTP copy.
Follow symbolic links
Displays symbolic links and NTFS junction points as if they were their target. This includes whether they will be shown as files or folders, their size, their last modified time, and their attributes.
Maintain DOS 8.3 aliases 
Tries to keep the same short (DOS 8.3) filenames when copying files.
Copy NTFS file permissions
Copies security descriptors of files on NTFS file systems under Windows 2000 or newer. This feature does not preserve permissions of files edited from Text Compare sessions.
Copy creation dates
Preserves original creation date of a local file when making a copy.
Automatic refresh
Set this option to periodically refresh the folder comparison.