You should enter both of the 1099-R forms you received.
There should be appropriate Codes in Box 7 of each that explain what happened.
Be sure to carefully read the follow-up questions after each of your entries.
If the money was rolled over within 60 days, there should be no tax consequences to you.
Here's more info on How to Enter 1099-R and Box 7 Codes on Form 1099-R.
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