I'm slowly giving up on nix darwin as I experience constantly the same, reoccuring issue, where my iCloud (container?) gets broken. Always the same story: My nix darwin flake/config works perfectly fine, but at some point I will have to run "rebuild switch" and reboot my system and almost all of my iCloud folders are gone from the iCloud Finder tab. The only ones persisting are the ones I created myself after the last time I reinstalled my macOS. The only way for me to fix it is when I delete my user account, create a new one, reinstall Nix and start from scratch, but it's getting exhausting.
My full config can be seen here.

Any idea what do I do wrong and how can I fix it without having to recreate new user account/reinstalling my system? Can it even be fixed? I admit I'm new to this all, documentation doesn't say much and I can't find anything googling.

I think this time the culprit was the 'raycast-symlinks.nix' file. I noticed it only after I ran rebuild switch with this command I use alias for:

sudo -H darwin-rebuild switch --flake ~/.config/nix/nix-darwin#macbook

... and rebooted.