iCloud has deleted files in my Desktop (...kind of?)

I'm a college student and have been using my Desktop hooked up to iCloud as an easy way to have all of my files on every device. Recently, in the time directly following a hefty build for my final project, my iCloud storage (200GB plan) filled up, and now the majority of the files aren't there when I open the folders on my Desktop.

Weirdly, they still show up on my iPad and my iCloud drive on the browser. This makes me think it might be a problem with my Mac rather than iCloud— I also upgraded to the 2TB plan (which was going to happen eventually), but the issue is still present. Worst case scenario, I can redownload the files from the browser, but them existing on other devices suggests that would just duplicate them.