I started having some really odd things happen when I would download a folder from my server via SFTP in Filezilla. I'm running Kubuntu 14.10.

The file looks like it downloads fine within Filezilla, no error message or anything but after it is done downloading the folder is missing on the server and in the Download folder. They are both just gone.

I have downloaded the file again to the server and then did the transfer again to the client Download folder, and again, it disappears. The odd thing is that it doesn't happen with all the folders downloaded, though they are all from the same source and nearly identical, just slightly different file sizes within each folder.

I found that if I access the server via HTTP I can download the file to the same destination folder and it is fine, no problem.

Sorry for the aside, but are you aware that Kubuntu 14.10 went end-of-life in June 2015?

If I were you, I wouldn't be putting that distro anywhere near the internet. Is there a specific reason that you're still running it?

I don't know why I typed 14.10 , It's the LTS 14.04.xx. It's been updated almost daily.

No problem then. I hope someone is able to resolve your unusual problem. Perhaps try out a later version of Filezilla? (there might be one in a PPA somewhere or you could compile one)

have you tried to recreate the problem with sftp itself (CLI, owned by openssh)? or scp?
so far all i see is a filezilla problem.

i wouldn't use that software if you paid me for it.
on linux you just don't need it, multiple more elegant solutions exist: NFS, sshfs, hell, even samba would be better than filezilla.

in any case, please show us something to work with.
you have been here long enough to know what.