It's definitely not a clear cut issue. https://reason.com/volokh/2017/08/26/is-accepting-a-pardon-an-admis/

In terms of Flynn's case, this section seems the most relevant:

Indeed, some pardons expressly state that they are based on the pardoner's decision that the defendant was actually innocent; and some legal rules expressly contemplate that—consider, for instance, the federal statute that provides for compensation of the unjustly convicted, which allows a plaintiff to prevail by showing (among other things) "that he has been pardoned upon the stated ground of innocence and unjust conviction." UPDATE: The Justice Department Standards for Consideration of Clemency Petitioners also expressly contemplate the possibility of "pardon on grounds of innocence or miscarriage of justice," though they unsurprisingly note that such applicants "bear a formidable burden of persuasion" (since the Justice Department's strong presumption is that people convicted in federal court were indeed justly convicted).