Winscp

Перезаписывать файл можно, но нельзя менять его аттрибуты если ты не владелец. Поэтому при перезаписи файла не принадлежащего пользователю, от которого зашел пользователь с winscp, то он увидит сообщение угрожающее. Хотя файл сам обновится.

Во FreeBSD не владелец не может менять аттрибуты. Какие? Права и дату.

Вот тут флажок "Ignore permissions errors" поставить http://winscp.net/eng/docs/ui_transfer_custom или можно сбросить Preserve timestamp и Set premisson. От них и лезут ошибки.

Note that while you may have rights to overwrite the remote file, you may not have rights to change its timestamp. See Ignore permissions errors. With FTP protocol, preserving timestamp of uploaded files may not be supported.

Upload of file .. was successful, but error occurred while setting the permissions and/or timestamp. If the problem persists, turn off setting permissions or preserving timestamp. Alternatively you can turn on 'Ignore permission errors' option. You get this error, when a server fails to update file timestamp or permissions for some reason: On some systems, you need to be an owner of the file (write permissions are not enough) to modify its permissions or timestamp.

Whatever the reason is, you need to turn off Set permissions and Preserve timestamp options or turn on Ignore permission errors. Note that you cannot disable preserving timestamp for synchronization, unless you turn off Modification timestamp comparison criteria. When using scripting, add -nopreservetime and -nopermissions switches to put command.

FAR
если это из комадной строки запускает FAR, то ему туда дописать -nopreservetime и -nopermissions

Note that while you may have rights to overwrite the remote file, you may not have rights to change its attributes (permissions and timestamps). If you upload set of files, where for some you do not have the rights, you may want to check Ignore permission errors to avoid being prompted with error message for each of them. This option is supported with SFTP protocol only.

With FTP protocol, setting permissions during upload is not supported. You can change permissions explicitly after upload.

См. также
http://winscp.net/eng/docs/message_preserve_time_perm