The election to report accrued interest must be made on a timely filed return (including extensions). You cannot go back and amend the decedent's return for this. You will have to amend the estate return. Hopefully the estate made enough distributions not to have to pay income tax. With this amount of interest alone, you are looking at the 39.6 bracket. If it's not too late, perhaps the bonds themselves can be distributed to the beneficiaries. They will have to pay tax on the accrued interest, which they will have to do anyway if the estate has been distributed, but at least they won't have to go back and amend their own returns. Going forward they will just have to pay tax on the interest accrued each year, but that's not your problem unless they are also your clients.
I am working on one right now where bonds are still earning a guaranteed minimum of 4 percent. The beneficiaries would be foolish not to want the bonds instead of cash--where can you get risk-free returns like that today? Fortunately in this case I can declare the interest on the deceased's 2016 return, where it will be mostly negated by medical expenses.