Click Tools > Synchronize Folders, then click the Advanced button to display additional synchronization options.
For matching filenames always
Use this setting to control the action taken by CuteFTP Pro when synchronizing files with identical names. The default action, Use global overwite settings, can be adjusted for all files in Tools > Global Options > Transfer Settings > Smart Overwrite.
Overwrite copies the file with the more recent date (this is the behavior demonstrated in the above example).
Numerate will copy both files and number them to distinguish between the two.
Skip ignores matching files, and only transfers those files not yet present on the other system.
Remote file names that differ only in case
Use this setting to tell CuteFTP Pro what to do with files having identically-spelled but differently-cased names. You can choose: Transfer first file only and skip others, numerate files, or show rename prompt. Since Windows file systems do not support differently-cased file names, you may want to use this option when working with file systems that do (like Unix).
Ignore symbolic links
Select this option to prevent CuteFTP Pro from following symbolic links when mirroring subfolders. This option should be left on unless symbolic links are absolutely needed. If you disable this option and a symbolic link points to a spot further up the folder tree from where the mirroring began you can get stuck in an infinite loop.
When one-way mirroring, delete destination file if it does not exist in the source folder
Select this option to make the mirrored folder a strict duplicate of the source folder. This will update old files and delete unused files. If you disable this option, any extra files present in the mirrored folder will be left in place.
Always prompt before deleting
Disable this option to turn off the pop-up box that asks if you're sure you want to delete a file. If you plan to run synchronizations automatically, clear this check box, so that no one has to click OK before files can be deleted.
Force Binary transfers
Select this option to compensate for a problem that occurs when trying to synchronize ASCII files residing on UNIX file systems. Windows and UNIX differ slightly on how they store ASCII files, especially with regards to the End Of Line (EOL) or line breaks in ASCII documents. This difference causes an otherwise identical file to be seen as “different” when performing a synchronization tasks, due to the difference in size.
By forcing performing Binary transfers, all files are transferred in binary mode, which would mean that an ASCII file residing on a local system would be transferred to the remote server with its EOLs intact. Some Web servers can accommodate for this while others may not. This could result in an html or other ASCII document not being displayed in the end user’s browser.
It is best to experiment with the two options if you are unsure of what to choose. By default, force binary has been turned off, as extra traffic might be acceptable, while conserving EOLs in a UNIX environment may not.