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The $12000 you put back in can be counted as a rollover but the $4000 (even though it was withheld for tax) is going to be taxable to you.
The form 5498 just shows that the $12000 was put in the IRA. You can still show in your return now that $12000 was rolled over. By the time the IRS looks at your return the 5498 will be available.
You need to report the full $16k on line 16a and then the $4000 on 16b.
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