Synchronization of files means to select most recent version of file (the last modified by user) and copy it to the other synchronized folder (or folders). Deletion of file is considered as type of file modification. Thus if user removes file.txt from FolderA after synchronization with FolderB file.txt will not exist in both folders. This is different from classic file backup algorithm.
The last version of a file is not nessesarily means greater file modification time. Sometimes you may decide to draw back and use old version of document that usually has older file file modification time. Unlike other file synchronization software Synctoy recognizes this situation correctly and will spread that old version on other folder(s) involved in synchronization.
In order to achieve better performance, Synctoy doesn't read each file to recognize difference. Instead it uses filesize and file modification time pair to detect if 2 files are different. Filesystem filetime resolution and timezones are taken into account. Note: file modification time is used to recognize the files are different. Synctoy do not make decision which file is the last version at this point.
File attributes are copied during file synchronization process. Old version of the file is removed.