Flynn probably gave the FBI useful information about Michael Cohen.
Remember how Cohen hand delivered a Ukrainian "peace plan" to Michael Flynn a week before Flynn resigned? So maybe Flynn's cooperation helped Mueller's office get the search warrant on Cohen's emails.
This article was from February 2017:
https://www.nytimes.com/2017/02/19/us/politics/donald-trump-ukraine-russia.html?mtrref=www.google.com
A week before Michael T. Flynn resigned as national security adviser, a sealed proposal was hand-delivered to his office, outlining a way for President Trump to lift sanctions against Russia.
Mr. Flynn is gone, having been caught lying about his own discussion of sanctions with the Russian ambassador. But the proposal, a peace plan for Ukraine and Russia, remains, along with those pushing it: Michael D. Cohen, the presidents personal lawyer, who delivered the document; Felix H. Sater, a business associate who helped Mr. Trump scout deals in Russia; and a Ukrainian lawmaker trying to rise in a political opposition movement shaped in part by Mr. Trumps former campaign manager Paul Manafort.
SNIP
After speaking with Mr. Sater and Mr. Artemenko in person, Mr. Cohen said he would deliver the plan to the White House.
SNIP
He said Mr. Sater had given him the written proposal in a sealed envelope. When Mr. Cohen met with Mr. Trump in the Oval Office in early February, he said, he left the proposal in Mr. Flynns office.
Mr. Cohen said he was waiting for a response when Mr. Flynn was forced from his post.