Having worked with After Effects for many years, I've never seen this happen. While I was working, I suddenly realized that 90% of the folders and the imported assets within them, went missing, yet my compositions were still in tact, and nothing was coming up as "footage missing". I am not sure if it was a key stroke that I accidentally made, or what, but like magic they weren't there. So when I right clicked on my "Hero Composition" to "Reveal Composition in Project", it would suddenly appear in the project window, no longer in my usual top folder of "Hero Compositions". So luckily, it didn't effect my project as a whole, apart from the management and organization of the project. But I also want to share how I got them back. I "revealed in Project" one more main comp, and then placed them in a new Hero Comps folder. Selecting them, I collected the files for those comps, which it did, and while watching the progress bar finish, the Mac's spinning color wheel appeared, and then all of a sudden, all my folders re-appeared again, like magic. Now that I think about it, I probably could have just closed the project and reopened it. And perhaps it was a Mac issue, and not even related to AE, but I wanted to share the predicament in case anyone came across and wasn't sure how to resolve it.
I bet that's what I did. Interesting. I've never used the search bar in the project window, so I wouldn't have thought about that possiblity, but good to know. I am so anal about how I organize my project and where I place things. When I teach AE, that is the one thing I try to drive into the students minds as much as possible. Thanks.