FTP Transfers keep asking me about existing files even when they are not
Solution 1:
It seems like Filezilla is disconnecting / getting disconnected and causing the partial file upload.
Go into "Edit" -> "Settings" -> "Transfers" and tune it down to one and try the test again. It may be that the server doesn't like simultaneous transfers. If it is set to one then you may have another issue.
If it works on one transfer at a time tune it up to two or three and try again. You can keep testing to find the max.
It could also be that the server doesn't want you to stay connected for long, in which case one fast connection would be better than many slower connections.