The FTP client will note if the file was uploaded successfully or not and the final result size of the transfer. Check the Cyberduck FTP logs to learn more about status of your upload and any issues encountered. If there was a problem, upload can be started over (when only 0 KB of data transfered) or resumed (if some has loaded, but not all - an interrupted transfer). You might also want to try a different client such as FileZilla. Please be aware the the size limit for data upload is 50 GB per file and also that FTP, not SFTP, must be used.
More about how to upload data to Galaxy: Loading_data
Testing with a smaller dataset, as Martin suggests, is a great way to troubleshoot issues with FTP clients.
Thanks, Jen, Galaxy team