That's your job.
The great thing about coding agents is that you can tell them "change of design: all API interactions need to go through a new single class that does authentication and retries and rate-limit throttling" and... they'll track down dozens or even hundreds of places that need updating and fix them all.
(And the automated test suite will help them confirm that the refactoring worked properly, because naturally you had them construct an automated test suite when they built those original features, right?)
Going back to typing all of the code yourself (my interpretation of "writing by hand") because you don't have the agent-managerial skills to tell the coding agents how to clean up the mess they made feels short-sighted to me.