My local file was deleted while the remote file was present. Which settings should I change on the Auto FTP manager to prevent this from happening?

Hi,
The last modified date on some of my files was 2003/6/1. However, when they were uploaded to the web server, the last modified date changed to today's date. Will Auto FTP manager try to synchronize the files even if they are not modified?
Please advice on how Auto FTP manager compares the files- by date, size or any other method?