The prevailing theory is that Mueller is using the threat of possible future charges as a way to ensure Flynn's long-term cooperation now that he's helping prosecutors build their criminal case against Trump and his family.
Over the holidays, I happened to run into an old acquaintance who has worked in the U.S. Attorney's Office and handled complex criminal prosecutions. He told me of an interesting theory about Flynn that is fairly widely held in amongst prosecutors.
This theory holds that Flynn knows something so damning to the White House and utterly unknown to the public at large that Mueller doesn't want to tip his hand in the public documents
The theory further posits that this incredibly damning evidence would ensure that Trump's son-in-law, Jared Kushner, would spend decades in federal prison if convicted. Thus, this idea concludes, Mueller's team will try to use this explosive evidence to flip Kushner so that he testifies against the President.
Now this is just a speculative theory amongst prosecutors who are watching what they think are subtle tells coming out of Mueller's office. They could be ridiculously wide of the mark.
But if this is true -- and it's certainly consistent with how Robert Mueller broke complex criminal cases -- then we ain't seen nothin' yet in the Russiagate Soap Opera.