Computers are generally really great at automating things so that you don't have to do things manually like this. I sometimes feel sad when I read that someone spent two or three hours telling a computer to do the same thing to hundreds of files, one after another. Usually there is a command or tool that would tell the computer to take care of that entire repetitive task—it's one of the things computers do best!
I regularly copy lots of files from one places to another on my computer (or one computer to another) using various tools, and when I do that I don't have to select or choose the individual files to be copied or transferred; i can just say "this entire folder/directory and everything within it". So I believe the answer is ultimately yes. 
The choices involved might be a bit daunting, especially since there are now dozens of options, but we do have a list on this forum of "Web hosting who support Let's Encrypt"
which collects various kinds of web hosts that support Let's Encrypt in various ways by making it convenient (and normally free of charge) to get, install, and renew a Let's Encrypt certificate so as to allow secure HTTPS connections to customers' sites.