Depends on what files you are trying to transfer by ftp.
FTp transfer is achieved by various dedicated homebrews, but that means atmosphere must be running. And you can't update atmosphere or its modules while they are running. Updating atmosphere has to be done via usb UMS connection in hekate.
I also think fixing archive bit can only be done in hekate. Someone will correct me if I'm wrong, but I don't know about any other homebrew able to do it.
It's also possible your ftp homebrew requires an update, or you have wrong settings on your PC side app (filezilla?).