Split a 6,000-line utils module with an agent

You inherited a 6,000-line Python utils.py that about 200 modules import from. Its functions call each other in tangles, and a few of them import modules that import utils back. You want an AI agent to help split it into cohesive modules without breaking the 200 importers.

How do you direct the agent and sequence the work so it does not turn into weeks of regressions?