A little update as of yesterday:
I've been paying for the 200 gb storage plan since about 2016, and have never had an issue with my files disappearing from iCloud Drive, which is why I've never considered archiving files and backing up that archive elsewhere (this is my fault). After seeing this thread and looking into this issue all over the web, I couldn't find anything that addressed recovering only the missing files (e.g., pdf's, jpeg's, png's, etc.) from iCloud Drive. None of my other Apple/iCloud data is missing; all calendars, messages, password, photos, videos, notes, reminders, etc. are all still completely intact (thankfully). So I ended up calling Apple Customer Service about this yesterday and was on the phone with two reps for close to an hour. Although they were extremely patient and tried to be as helpful as possible, they couldn't identify the cause of the issue or how to remedy it, so they had to send my problem to their Engineering team. Although the service rep was great, ultimately the solution was this: we will try to recover your missing files, but we can't guarantee we'll find them. In the future, make a separate backup of all the files saved in your iCloud Drive and any other important data, and store that archive/backup file elsewhere so this issue can be avoided again.