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After a defendant, with the court’s permission, withdraws a guilty plea, the case normally reverts to the point before the original plea. The defense can hammer out another deal with the prosecution or go to trial. If the reason for the withdrawal undermines the prosecution’s case (as in the instance of newly discovered evidence of innocence), the judge might even dismiss the charges. But withdrawing a plea doesn’t always end happily: There’s typically no guarantee that the defendant won’t receive a harsher sentence if convicted (again).
Sauce: https://www.nolo.com/legal-encyclopedia/withdrawing-guilty-plea-criminal-case.html
This may be why Gen Flynn is maintaining his plea.