Sally Yates (then the deputy U.S. attorney general) confirmed that Obama (as of January 2017) knew that Michael Flynn was being investigated. Obama also was confirmed to be in the discussions (with James Comey) of whether the case against Flynn should go forward. It is safe to assume that James Comey proceeded with the case with Obama’s blessing.
Didn’t a Lisa Page text say “ POTUS want to be kept informed”? re: Crossfire Hurricane.