Both copies of a file, source and target, cannot be retained. As Secure Copy is not a versioning system, there is no way for Secure Copy to be configured so that the source file is copied to the target and also maintain the target file as well, creating 2 different files.
With the default Synchronization settings (Copy only changed source file to target), only source files that are newer than the target files, or have a different size, will be copied over. If the source file is newer than the same file on the target, the newer source file is copied over, overwriting the target file. If the target file is newer than the source file, and the file sizes are the same, nothing is copied over and the target file is maintained as is. If the file sizes are different, even if the target is larger, the source file is copied over, overwriting the target file.
This behaviour can be changed. If you select the 'Overwrite target files even if they are newer than the source' Synchronization option, then the source file will always be copied over and overwrite the target, regardless if the target file is newer.
