The custodian is required to report in box 2 of the Form 5498 the value of the rolled-over shares as of the date of the rollover contribution, which may (or in this case, is) different for the value on the date of the distribution. This is why I suggest including an statement with your tax return to explain why the value on in box 2 of the Form 5498 shows a different amount than the amount actually rolled over (the value on the date of distribution; if there is a rollover of only part of the distribution, the dollar value that you must indicate to TurboTax as the amount rolled over is the dollar value on the date of distribution). It's likely that the IRS's automated system implemented in recent years will flag the discrepancy and require an examiner to determine whether or not to treat it as an underreporting of income. The explanation statement that you include with your mailed tax return will generally be sufficient to satisfy the examiner. If the examiner needs additional supporting documentation, they will ask for it.
CFR 1.401-1(b)(1) indicates that the distribution is not taxable if the entire amount of cash and property distribution (only property in this case) is rolled over. To effect reporting of a nontaxable rollover, you indicate to TurboTax that the entire distribution was rolled over (assuming that there will not have been any other distributions from this IRA that were not rolled over). What is reported on your tax return is the net taxable value, $0 in this case, not the dollar value at the time of the rollover. It's the IRS's automated system that compares the amount of the distribution, the amount reported as taxable and the amount reported by the receiving custodian in box 2 of Form 5498 to determine if there is any discrepancy. It this case there will be a discrepancy that your explanation statement will address.
