I have the same problem, but I found a simple workaround that maybe work for you (in my case I only had to transfer and overwrite 3 files):
First, I checked if the server lets me upload new files instead of overwriting them, as well as removing them. So I made copies of the files with other names (i.e. index-copy.html) and FileZilla allowed me to upload them. Then I deleted the original files and renamed the new ones to what they were supposed to be. That's all.
I still need to contact my hosting providers, but at least I've already made the changes.