Hard to say what happened. It may have just been some kind of glitch, either with some app (like AVG) that went hayware and deleted a bunch of files, or with the system itself.
Although I realize it may be a monumental pain to redo the photo organization in Google Photos, it still may be worthwhile, because it will make photo storage so much easier in the future. You won't have to worry about transferring photos from old phones to new phones, and there are significant advantages to how Google Photos organizes photos. I like how one photo can be in multiple albums without having to duplicate it -- if you did that on a phone's local storage, you'd have to create new copies of the photo to place them in other directories. Most importantly, the search function in Google Photos is phenomenal, and is often an easier way to locate a specific photo than trying to figure out which album it's in. You can search for specific people or pets, events, objects, holidays, locations, etc.