There are at least three methods.
Hacking into the PCB file as Jonathan suggested is one of them, and this used to be common several years ago, but it’s rarely needed these days, as most of the gaps in KiCad’s GUI have been fixed. (But it still can be a quick option do do a search & replace in a text editor).
If you’ve made your holes out of via’s, as ronsimpson guessed, then have a go at: Pcbnew / Edit / Edit Track & Via proterties.
If you have used footprints for your breadboard look-alike, then the best way probably is to first modify the footprint, and then update all footprints on your PCB with that new footprint. If you’ve used some default footprint then you first have to copy it into a (probably best: a project specific) new library, because KiCad’s default libraries are read-only.
After that, it depends a bit whether you first made a schematic or just placed footrpints on the PCB.
For more on library management, the FAQ part of this forum has a quite big list of tutorials on specific subjects.
https://forum.kicad.info/search?q=library%20management%20category%3A19