So there is a pretty obvious analogy in chemistry: activation energy.
https://en.wikipedia.org/wiki/Activation_energy
The ELI5 version is that atoms are all trying to find a comfy place to be. Typically, they make some friends and hang out together, which makes them very comfy, and we call the group of friend-atoms a molecule. Sometimes there are groups of friendly atoms that would be even comfier if they swapped a few friends around, but losing friends and making new friends can be scary and seem like it won't be comfy, so it takes a bit of a push to convince the atoms to do it. That push is precisely activation energy, and the rearrangement won't happen without it (modulo quantum tunneling but this is the ELI5 version.)
In the software world, everyone is trying to make "good" software. Just like atoms in molecules, our ideas and systems form bonds with other ideas and systems where those bonds seem beneficial. But sometimes we realize there are better arrangements that weren't obvious at the outset, so we have to break apart the groupings that formed originally. That act of breakage and reforming takes energy, and is messy, and is exactly what this author is writing about.