This happened to me this past week—and just like you said—I hadn’t deleted anything!
I hadn’t used my laptop in weeks, turned it on and pop-ups began. I just kept closing the pop-up without reading thinking it was updating or something and then saw it said my photos were deleting from all my devices!
It was doing it randomly—each batch contained unrelated photos from all different times.
I recovered them all, however, it started again today about 30 minutes after I turned on my laptop. I probably wouldn’t have noticed, but I was keeping an eye on my photos on my phone and iPad. No iCloud popup this time but I could see on my phone that 83 random photos were placed in the deleted folder (which was previously empty).
So apparently just restoring the photos is not a fix. What’s going on?
Also, when I open iCloud using the tray icon, the iCloud Photos settings menu overlays the main ICloud app screen and the photo menu overlay can’t be closed without closing the main iCloud app screen.
There’s got to be more to this.