cuteFTP tends to drop files during upload when an error is encountered. Errors such as too many connections to the server etc.
Instead of transfering folders, try to transfer iniviual files by highlighting all of the files to be transfered the clicking upload (download). Then if you have a problem, you can just start with the problem file. The queue will display error messages next to files that were aborted. Just remove the status of the problem file (usually at the top of the list) and click transfer queue.
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Let me know if you need more help. Always around for assistance.
vujsa
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