I cannot help you with server side issues, sorry!
I can tell you that each course with files in it has a folder in the moodledata directory. You can figure out which course ID goes with the course (look at the URL at the top when you are in the course, it will include the ID). Then look for the same folder in moodle data. You can copy and paste the files through the operating system.
I feel that I am not making very much sense, sorry! Maybe you can figure it out anyway!
atw
Backup and restore
Import does not copy course-files
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