Ahhh, gotcha, NotSuper. I'm switching out of stupid mode now. heh
I don't think those cities were ever shown being returned to their homeworlds, at least not by Superman.
The Coluans revolted against the computer tyrants so they arguably had access to all the technology and shrunken cities, esp. since Vril Dox had a 12th-level intelligence compared with the tyrants' 10th-level ones. While not shown, arguably the Coluans, or at least Vril, restored those other cities. I can't honestly see them keeping those shrunken victims around after asserting their own justice for themselves.
The shrunken cities were never shown either in the present or 30th century Colu, so I suspect that's what happened.
That's a good theory, but wouldn't Superman have had Kandor restored by the Coluans if that was the case? I think Superman would've just returned the shrunken cities to their home worlds, maybe even restoring the inhabitants after he restored Kandor.
Was there ever a story, which re-told the original encounter between Superman and Brainiac? If there is an answer to this question, we'll find it there.