I don't think so. Flynn has his liberty now, and even if Sullivan goes ultra nutty and files a criminal contempt charge to run the clock, Flynn will be free while that case is prosecuted, and eventually, that case won't stick.
The judicial branch is holding Flynn in its clutches, to help swing the election.. The press gets narrative of "Barr bad, even courts agree."
When Trump is re-elected, nothing the courts do on the Flynn subject will redound to the harm of Trump. At that point the courts will proclaim they are pure as driven snow, and of course it is wrong to hold up the Flynn case.
There is though, truth in what you posit. Flynn's case has to end in Flynn's favor in order for him to have a malicious prosecution claim. That's already happened. If there is a pardon, it will not be for "lying to the FBI." The government has asserted that the FBI had no justification to interview Flynn in the first place.
If there ever is a pardon from Trump, it will be for contempt issued by the court, on account of Flynn filing then asking to withdraw his guilty plea. That's a separate (bogus) case, and if Sullivan wasn't a judge, he'd be setting himself up for a claim of malicious prosecution.
Thanks for your take on Flynn case. A real travesty