Declassified evidence and interviews of the FBI agents in charge of the case corroborate that they thought Flynn was innocent, and actually tried to close the case in January 2017. [1 - contains links to declassified evidence] FBI management overrode their decision, and tried to arrange another meeting to fish for something to nail him on.

Here is the declassified note of the agents in charge of case trying to close it from Jan 4 2017. [2]

[1] https://justthenews.com/accountability/russia-and-ukraine-sc...

[2] https://justthenews.com/sites/default/files/2020-04/FBIFlynn...