If you never received the funds then Fidelity should not have issued a 1099. One option is to report it as shown on the 1099 but indicate it was rolled over within 60 days. This gets it out of taxable income, which is what you want. A concern here might be if there is another 60 day rollover within a year; if there isn't then you shouldn't have a problem. Don't know if you can attach a statement to the return indicating it was a trustee-to-trustee transfer?
Bottom line for me would be: 1) show the 1099 on the return so it isn't kicked out , and 2) get the money out of taxable income. I would definitely not report the income and rely on the IRS to back it out of taxable income by matching to receiving institution's 5498!