The way I do this is I task the agent with writing a script which in turn does the updates. I can inspect that script, and I can run it on a subset of files/folders, and I can git revert changes if something went wrong and ask the agent to fix the script or fine-tune it myself. And I don't burn through tokens :)

Also, another important factor (as in everything) is to do things in many small steps, instead of giving one big complicated prompt.