Oxford Dictionaries Online gives the following definition for the phrasal verb shake down:
become established in a new place or situation; settle down
And it gives the following example sentence for this meaning:
It was disruptive to the industry as it was shaking down after deregulation.
I know shaking down here means "restoring". But how could shaking down be a disruptive thing? Or do the two its in the sentence have different denotations?