It means what it says. Either you do not have enough permissions to modify the files themselves, or the directory, where the files are located.

I keep getting this message:

Error, cannot overwrite remote file.

Permission denied. Error code: 3
Request code: 3

What does this mean?

I have never had this kind of problem before.

A lot of my files has gone missing now from the web and I really want to upload them again as soon as possible but at this moment I can't do anything. Not upload files, not delete files.