As far as I can read, in the first instance you have to see if you are doing it by https, see your credentials and the permissions in the proxy.
To see where the problem is, you have to analyze in which process the problem starts to occur. Depending on this by discards you are solving what interferes with your work.
As you are told, it is best to use GIT to upload the files to the server, the problem is that not all servers have GIT installed.
You can try git-ftp
and see if it's what you need: link I have never used it, so I can not tell you if it's going well or not. I leave you a small tutorial in Spanish: link
Another option is to use tools such as link , the inconvenience is that they are paid
But since I do not want you to run out of answers and try to help, you can read this tutorial of changes in the repository