According to the wiki you should run nix-store --optimize as root.
Weird, I don’t remember ever needing to do that. But I tried it, and it fixed the error:
[fisher@workshop ~]$ sudo nix store optimise
Password:
warning: the group 'nixbld' specified in 'build-users-group' does not exist
[fisher@workshop ~]$ nix store optimise
[fisher@workshop ~]$
I always get the nixbld warning when I run nix commands as root. I think it’s because I have a single user installation. But anyway, re-running nix store without sudo worked, so I think I’m good now. Thanks!