Flynn, whose sentencing is scheduled for Dec. 18, pleaded guilty in December 2017 to lying to the Federal Bureau of Investigation about his conversations with then-Russian Ambassador Sergey Kislyak during the presidential transition period from election day 2016 to Trump's inauguration in January 2017.
Prosecutors suggested no prison time after 19 interviews with Flynn.
Longtime Donald Trump associate Roger Stone arrives to testify behind closed-doors as part of the House Intelligence Committee's investigation into Russian meddling in the 2016 election, September 26, 2017.
But according to memos penned by Comey, President Trump tried to protect Flynn by asking Comey to let the investigation into his false statements go.
"Those who said the president's warm and complimentary tweet constitutes witness tampering should be reminded that I have never been contacted by any investigative body and therefore, by definition, this can not be true", Stone told the Daily Caller's Saagar Enjeti.
Cohen's lawyers, meanwhile, submitted a sentencing memo on his behalf last week that contained a slew of bombshells about Trump and his interactions with Cohen a year ago and before the 2016 election.
The special counsel pushed back Flynn's sentencing multiple times "due to the status" of the investigation.
He later pleaded guilty to lying to the Federal Bureau of Investigation over his relationship with then-Russian ambassador Sergey Kislyak.
Flynn became the first high-ranking Trump associate to agree to cooperate with the special counsel's prove when he pleaded guilty on December 1, 2017.
Though prosecutors withheld specific details of Flynn's cooperation because of ongoing investigations, their filing nonetheless underscores the breadth of how much information Mueller has obtained from people close to Trump as the president increasingly vents his anger at the probe - and those who cooperate with it. Most notably, Trump's former campaign chairman, Paul Manafort, aggressively fought the investigation and is now facing the possibility of a lengthy prison sentence after his cooperation agreement recently fell apart over allegations that he had lied to investigators.
He was forced out over revelations that he had discussed lifting United States sanctions on Russia with the Russian ambassador to Washington before Mr Trump took office, and that he lied to the USA vice-president about that conversation. Flynn, who resigned following reports that he misled White House officials about his contacts with Russia, was seen attending the 10th anniversary of the Russian television network RT in 2015 where Russian President Vladimir Putin gave a speech.