Now, it seems to me highly unlikely that Flynn deliberately lied to Pence, which is not to say that he didn't somehow mislead him without malice aforethought. It's not hard to believe that the topic of sanctions or the current dust up with the expulsion of diplomats, etc., came up in the course of the five conversations. Nor is it hard to believe that some sort of signaling take place. In fact, it would be very hard to believe that the discussions were all just hey how ya doing. But talking about issues in itself is not illegal. I don't know what the communications between Flynn and Pence were, but it's easy to think that it was more along the lines of a general assertion that they were routine and it's possible that sanctions never came up.
On the flip side, I wonder why the administration didn't have some clarification or assertion ready for the Sunday talking heads. Possible explanations are there is some dirty laundry they are not ready to clean or they are trying to keep the chaos up either just for distraction or to see if one of the leakers identifies himself. Or, maybe they see that the ball is still in the leakers' court and wait to see what drops?
Finally, the motivation of the leakers themselves. Is there really some light that they are trying to shed on potential wrongdoing? If that's the case, why not just leak the transcripts? They may nominally be classified, but I'd be deeply skeptical if there is any material that in its disclosure would be harmful to the National interest. These are not the Pentagon Papers. If there are names, they can be redacted -- that is not the substance of the allegations. If there was material that was disclosed of a highly sensitive nature, that would have been the allegation itself, not a potential Logan Act violation. Perhaps the motivation was just to sow chaos and join in the general obstruction of the opposition in its sundry forms. Or, perhaps, it's merely to impugn Gen Flynn's character, an act of revenge against a man who has rubbed many in the IC the wrong way. Or some combination. However, if it turns out these allegations are unfounded, or so weakly founded that no charge can be brought (sanctions were mentioned, but generally and certainly without intent to contravene Administration policy), or deliberate intent for Flynn to intentionally deceive Pence can be demonstrated, these leakers will further damage the credibility of the larger IC and further add to the dupmster fire of "fake news" hysteria, which would be unfortunate.