In my son’s case, it was a Harvard class in Ancient Greek - he had “won” the choice of class through some classics program. He did not take the final exam; he took the National Greek Exam that is put out by the same people who do the National Latin Exam. He wrote an explanatory blurb that he "withdrew and changed to audit status, and took the NGE earning a silver level” and possibly his GC included in his letter that this made the most sense with his other classes that year plus MIT PRIMES or whatever other overdoing-it nonsense he was loading up on.
It’s not clear whether the Greek ended up helping, hurting, or being neutral. This was my DS16 who was a strong enough candidate that ultimately he got in everywhere he applied. And things have also changed in the past ten years.
I do think you have to be honest with all these schools. For instance, my DS was told that once enrolled for an AP class, even senior year, he had to take the AP exam. (Princeton told him this on a phone call when he didn’t want to take the AP Euro exam because he had the limit of history AP credits and he could earn money working that day instead plus get a partial refund of the AP cost which mattered to our budget. CC people still don’t believe me but what can I do; I heard the call and it’s true.)
The relevance of these stories to your DD is that she should be straightforward with all of her colleges about her story, and of course spin it as positively as she can, but ultimately make the full picture as compelling as possible.