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.
It shows in
https://www.supermanthroughtheages.com/tales3/greatest/?page=76 that Brainac never passed on the secret of enlarging the citites. So that leaves with what, that there where no bottled cities except those from earth and kondor at the time?
I've wondered did Brainiac shrink any more after his first encounter with Kal?