1. Create on localhost and server a empty folder
2. First create on localhost a file with with any content
3. Copy file from localhost to empty folder on server
4. Edit file on server with a editor, so its get a newer time
That can have plenty of reasons. Example; To make a hotfix which is already included in your localhost file, but that have more changes that make its current impossible to upload the whole file.
5. Now start a synchronisation direction server for final update all project files on server
Result: "No differences found"
Setting was "Comparsion criteria" by "Modification time"
Turn direction to localhost its found the differences. So this criteria find only "old" files, not one of both side is different.
That can make worst things to your project. I synchronize many folders and files and from time to time I must make hotfixes and later I want update all updated files.