Thanks for your reply, they were uploaded into the correct folder.
I did write to support, the problem is that Photodune automatically clear any files from FTP that haven’t been processed within 24hrs, of course it takes longer than 24hrs to upload 1200 files so it looks like by the time the files had finished uploading they had already been deleted.
Oh and in true Photodune fashion they hadn’t told anyone this!!
I uploaded over 1200 files by FTP on the weekend, none of them are showing up in my dashboard and there’s no ‘process’ option.
Any idea where these files have gone?