Duplicate photos if I sign out of iCloud and back in?

Hi, during the weekend, I experienced the problem I see reported by many people; iCloud on my Mac asks for the password, but typing it just returns the same request. After a while, it turned into saying I ad to generate an app-specific password for FaceTime and iMessages, which I did and that seemed to fix the problem. Next day, problem back, and various posts suggest a fix was to sign out of iCloud in System Preferences, and back in again, which I did.

It has so far fixed the password-asking problem, but it seems Photos is ready to upload a second set of my 28,000 pictures... I set it to pause for a day until I could figure out what's going on, but searching has not helped me figure out whether signing out of iCloud and then back in again will cause this doubling of my library in the cloud. Does anyone know? It seems strange, there could be several reasons why one would sign out of iCloud, so I'd hope it would figure out which photos are already in the cloud and don't upload these again...

Does anyone know how this works?