If you enter both Form 1099-R into your return, then both will be taxed and penalized. There is not a way to get around that if they are both entered.
My opinion is that one of the forms was sent in error since they represent the same loan. As long as you have documentation from when the loan originated and from the amounts that you repaid to justify that only one of the Form 1099-R should have been issued (meaning you only still owed the amount reported on one of the 1099-R and not both), then you should enter the Form 1099-R that was issued by the company who had control of the 401K at the time you left your job. The loan balance did not become taxable to you until the date you left the company.
If the IRS questions why both Form 1099-Rs were not reported, you should be able to provide your backup documentation to show that the one not included on your return was issued in error.
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