It is a missed RMD and she can't take it. You will have to file her taxes without the RMD and file a 5329 request for waiver and explain it was missed because she passed and that you took corrective action as soon as you discovered the issue. The IRS should allow the waiver due to the circumstances.
You'll calculate that penalty in Part 9 of Form 5329. To request a waiver, enter “RC” (for reasonable cause) and the amount of shortfall you want waived on the dotted line next to Line 54. Attach a letter to your tax return explaining the situation.
You will have to report it all on your tax return with the 1099-R when it comes. Just keep records in case the IRS asks - I really doubt they will.
I am very sorry for the loss of both parents.
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