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well yes, like i said, just a case of writing a small batch file. if you want to use ncftp for the sake of it, it appears to include an ncftpbatch command to accept jobs in batch, just check the docs for it.
Distribution: Debian Wheezy/Jessie/Sid, Linux Mint DE
The best is to write a small batch script. Use ncftput, in that way you can give login parameters etc on the command line. ncftpput can handle multiple files at once so you need only one command per directorty.
You can put the call to your bash script in a cron job.
This is so reliable that I once discovered that the script still was doing a succesful upload of something while the project had already stopped 2 years before...