When the purge function is enabled, Secure Copy compares the list of files on the Source and Target paths. If a file is present on the Target, the application presumes the corresponding file has been deleted from the Source volume and deletes the file as part of the synchronization.
This is expected behavior when copying between NTFS file systems.
However, .his and .cfg files on the NAS are part of the block level storage and are used as part of the file management on the device.
An upcoming verion of Secure Copy will contain an option to 'white list' files on the Target shares and paths. Files and folders in the list will not be purged from the Target device.
Until this release, a special build of Secure Copy 188.8.131.52 can be obtained from Quest Software Technical Support that includes this option.