If you could upload all your files, the question is: what then?
How are they added to courses? How do students access the files?
Moodle handles file management through the database - this ensures that there are no duplicate files and that only users with permissions can view the files.
However, you can create your own repository (https://docs.moodle.org/31/en/File_system_repository). This allows you to upload all your files via FTP. Following the procedure on the link I've added, as an admin you set up the repository, then the teachers can add files from the repository to the courses they teach. This will make the files available to students. But the teacher still has to add them to each course they teach.