If you have more than one 1099-R entered in TurboTax, you should be able to see this and know what you are deleting.
Navigate to Wages & Income->Retirement Plans & Social Security->IRA, 401(k), Pension Plans withdrawals (1099-R). Note that this is the navigation in the CD/download TurboTax product. The Online product may use different wording, but the general navigation should be the same.
When you enter the 1099-R section, if you have one or more 1099-Rs entered, you should see a list. "Edit" each one to enter and see it.
I am assuming that TurboTax asked if you wanted to delete a 1099-R ONLY because there were important fields missing, which would be consistent with a failed download.
Anyway, check them each and throw away (DELETE button or trash can icon) the one that doesn't belong.
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