File backups not completing

I have two separate self-hosted sites on WordPress. I have been using Cyberduck for *years* to back both of these sites up monthly. (Yes, I am also using the auto database backup as well.) Suddenly, since the start of the year, I am getting errors about halfway through the backups. The time out and then start over from the beginning. Thinking this was an error with Cyberduck, I installed and ran the BackWPup plugin and it’s giving me an error saying certain file names are too long. Any idea how to remedy these errors?