I went through a nearly identical situation in 2024 and wanted to share what I learned. The 45-day identification window under IRC Section 1031(a)(3)(A) is an absolute deadline -- the IRS and the Tax Court have consistently refused to grant extensions, even for natural disasters or other hardship. In Christensen v. Commissioner, the court held that the identification period is jurisdictional and cannot be equitably tolled.
When you miss the 45-day window, the exchange fails and the entire gain from the relinquished property becomes taxable in the year of the sale. For most people, that means a combined federal and state capital gains tax hit of 20-30% or more, depending on your income bracket and state. If you had depreciation recapture under Section 1250, that portion is taxed at 25% federally regardless.
One thing worth exploring with your CPA: if the failed exchange happened near the end of the tax year, you may be able to use an installment sale election under IRC Section 453 to spread the gain over multiple years, provided the proceeds were held by a qualified intermediary and not constructively received all at once. This does not fix the failed 1031, but it can soften the tax blow significantly.
Also, the IRS has issued guidance (Rev. Proc. 2018-58) extending deadlines for taxpayers in federally declared disaster areas. If any part of your timeline overlapped with a FEMA-declared disaster in your area, it is worth checking whether you qualify for relief. I have seen this save taxpayers who missed deadlines during hurricane season.
Going forward, the best practice is to have at least three backup replacement properties identified before day 30, using the three-property rule. Never wait until the last week. I also recommend using a qualified intermediary who sends automated reminders at day 20, 30, and 40.