I have had this same problem when garbage collecting on the root user. It happened to me twice. It was strange for me since I understood that Guix would NEVER remove any package that still had links to it.

What I did was try to boot with all entries presented on boot by GrUB. I usually found one that booted.

I am sorry I cannot reproduce this error since the 32 bit machine that I tryed garbage collecting previous generations on has died. I will test it on my other machines when I can manage to have a local substitute server to install offline from.