What is the word for making a set of conflicting rules/policies make sense and all agree with one another?
I think the right word for your sentence is conciliate, which means
To make or attempt to make compatible
This is very similar in meaning to reconcile which means
- To make compatible, harmonious, or consistent
or
- To make (two apparently conflicting things) compatible or consistent with each other
So your sentence would be
The new regulator conciliated the confusing mess of archaic policies so that there were no contradictions, and the requirements were now clear.
You could also use reconcile here, and it would have the same meaning.