You're right, there is no penalty on the 2023 contribution of $1,000 if you remove the excess before the due dat of the tax return. (I knew that !?)
you must also remove the earnings. so far it's not clear that the custodian did that for you.
"This treatment only applies if any earnings on the contributions are also withdrawn".
Pub 590-A (2022 edition) doesn't say what the treatment becomes if you don't meet the condition. If it does, I don't see it.
So for that situation, we are both confused.
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The penalty for 2020-2022 still applies to 2023 since the excess for those years was not removed in 2023.
The penalty for those years is resolved on 2024 Form 5329.
One approach is to assume condition is met and set 2023 Form 5329 Line 23 to zero.
She can revisit this decision in 2025 when you see the actual 2024 Form 1099-R.
At that time, she may decide there is nothing to do.
@kaitech3
