Well, that was after he got his wings, arms, and upper torso blown off. Granted, Chrysalis has enough AP to do that with far greater ease than Goku.
Anyway, Cell is a vastly more skilled and versatile fighter than Chrysalis with far greater stamina and range. At the same time, despite being vastly less skilled and versatile than Cell and lacking his impressive range, stamina, and Regenerationn, Chrysalis has energy blasts that are much, much more powerful. If this was a bloodlusted match, Cell would most likely win due to using his brain and employing battle stratagies he has never done before which had he used them in show could have let him win. With them both being in character, it becomes harder due to the fact that Cell rarely stratagises in battle. Chrysalis is only more powerful than Cell because of the energy blasts from her horn. If Cell could tire her out to the point where she couldn't fire any more, he could win. I guess the question is, can his stamina, skill, range, and Regenerationn enable him to tire her down? Also, can she get every bit of his body including the nucleus with her blasts? If the nucleus or any sizable portion of his body such as his lower torso survives, he will regenerate. All he needs is the nucleus or part of his torso or possibly a single intact bodypart to regenerate. You have to completely destroy the nucleus and reduce the rest of his body to chunky salsa to kill him. And that nucleus is extremely durable. If the nucleus survives while the rest of his body is destroyed, she'll fly off thinking she won, he'll regenerate, and he'll get a power boost. Than he'll teleport to her and continue the fight.