I would contact e-trade and ask them what substantially identical shares they assigned that they are claiming a wash sale? Are you sure they didn't assign the wash sale to the options as the wash sale cost basis had to be assigned to something, they don't just report it, they move that to adjust cost basis in other securities. Since it is a covered trade and reportable to the IRS, they should be able to substantiate their program and/or send a new 1099.... substantially identical could be very vague. Are you sure there was no spinoff or any other transaction with the shares. you should be able to go back to the sale date of the securities and see what happened within your statement. You can always adjust your basis and retain the records as proof. I have had issues with e-trade prior where they have refused to adjust and then 6 months later they realized they erred....
**I don't work for TT. Just trying to help. All the best.
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