After adding these folders, all video files show up in my Plex player alongside eachother, and the ordering is completely lost. The order that the folder structure gives is lost. How can I solve this?
Server Version#: 4.43.4
Player Version#: 1.61.1.3432-3929cb60
Alternatively you could consider organizing the files as a personal tv show where…
each course is its own show
each chapter is its own season
each file is its own episode
Though for that to work properly you’ll either need to embed some metadata into the mp4 files (and configure the library to prefer embedded metadata) – or name them manually inside Plex.
With an Other video type library and a naming as suggested by @BanzaiInstitute you’ll be more flexible (e.g. because Plex will pickup the titles of each file) and can group courses/chapters in collections if needed.
You should be able to set the library up as an Other video library and switch display on the library tab to Folder. That’ll be quite limited/limiting but it should work to let you drill into your folder structure and see the files as-is (unless you have embedded metadata interfering)