@dkocher commented

I cannot reproduce this against OpenSSH_7.4. What server software are you running?

d2f945c commented

Okay - so if login via command-line sftp from the same computer I'm running Cyberduck on, and use verbose, I get:

"OpenSSH_7.8p1, LibreSSL 2.6.2"

Once logged in to the SFTP server in question, if I type 'version' I get:

"SFTP protocol version 3"

I've emailed the operators of the SFTP server to find out more details of the software they're running. I could create a test account on that server for you if that would help? If so - please tell me how to securely send you account details.

d2f945c commented

Further to this - logging in with a command-line client and issuing a 'put' to the server in question over-writes an existing file. Using Cyberduck, concatenates the file. I've spoken now with the server provider, and they've checked the logs and said that Cyberduck is opening the file for writing without deleting an existing file with the same name in the directory first. Whereas, when we use the command-line client, the existing file is deleted before opening the new one for writing.

I have also changed the preferences in Cyberduck to 'Prompt' instead of 'Overwrite' and in this case CyberDuck does indeed prompt what to do - so it is checking for existing files and finding them. But, when I then click 'Overwrite' - it then still appends data instead of deleting first.

Finally - I turned on 'Upload with a temporary filename' - and that fixes the issue - in that of course CyberDuck now uploads to a temp file name, then issues a REMOVE on the existing file, before renaming the temporary file. The CyberDuck log shows this. Lines 160-185 below are with 'Overwrite' selected, and no temporary filename. Then lines 186+ are for with 'Use temporary filename' switched on.

160 OPENDIR
161 READDIR
162 READDIR
163 CLOSE
164 OPEN
165 WRITE
166 WRITE
167 WRITE
168 WRITE
169 WRITE
170 WRITE
171 WRITE
172 WRITE
173 WRITE
174 WRITE
175 WRITE
176 WRITE
177 WRITE
178 WRITE
179 WRITE
180 CLOSE
181 SETSTAT
182 OPENDIR
183 READDIR
184 READDIR
185 CLOSE
186 OPENDIR
187 READDIR
188 READDIR
189 CLOSE
190 OPEN
191 WRITE
192 WRITE
193 WRITE
194 WRITE
195 WRITE
196 WRITE
197 WRITE
198 WRITE
199 WRITE
200 WRITE
201 WRITE
202 WRITE
203 WRITE
204 WRITE
205 WRITE
206 CLOSE
207 SETSTAT
208 REMOVE
209 RENAME
210 OPENDIR
211 READDIR
212 READDIR
213 CLOSE

So 'Use temporary filename' at least provides us with a workaround at the moment, but I still feel the 'Overwrite' preference (whether prompted or set prejudicially) is not working correctly.

@dkocher commented

When a file already exists, we open the file in truncate mode specified in the SFTP protocol. This forces an existing file with the same name to be truncated to zero length.