FTP doesn't provide any method to ensure directories are 100% synchronized. You can choose to compare by date (be sure to enable preserve timestamps in the client), but this still has the problem that the remote server often only gives the date and no time (it depends on the server configuration). Alternately, you can choose to compare by file size, but because text files might be Unix format on one end and Windows format on the other, the size of text files is inconsistent. AFAIK, green means "these appear to match with available data but there's no way to tell for certain".
If it's for a business, I'd suggest you look into a server and client that support extensions for checksumming like XCRC, XMD5, or XSHA. If you demand something with some kind of certified
HMAC, you'll have to pay through the nose for it. There aren't many FTP servers and clients with FIPS 140-2 certification, but it's about the best standard out there. GlobalScape's CuteFTP Pro and MFT might be it for choices currently.
If what you're pulling has HIPAA or other encryption and integrity mandates, you should look at AS2 and ebMS instead of FTP.
