this issue might be because the user's files fall below the (configurable) threshold for the automatic transfer-to-alternate-name-then-replace-original behavior (100kB) ?
probably a good moment to mention
"Verify checksum of a remote file against a local file over SFTP/FTP protocol"
It might be a valuable enhancement if the Synchronize feature (or any SFTP/FTP transaction)
could have a "Verify" option. Should the user request file transfer verification and the server is unable to checksum/CRC, then a warning would be appropriate.
OTOH, with FTP and a server that supports XCRC/HASH/XSHA1/XMD5 extension(s), verification would be roughly equivalent as using SFTP alone. SFTP running on top of SSH2 has stronger integrity checking than over SSH1, so requesting file transfer verification should insist on at least SSH2 to the server (and then checking timestamp and file size post-transfer would be verification enough).