File Amended 1040? What would you do?

I got one of these letters last year for my late Dad's return for the previous year. The only reason I filed an amended return was that while IRS revised the income (DF forgot to include a 1099), they neglected to adjust the 2% figure for certain deductions. Otherwise, I wouldn't see a need to have filed it if I had agreed with IRS's revised tax.
 
I would think if there is no additional tax consequence in terms of tax due the IRS, I cannot imagine it would cause a problem to do nothing further. However, if there is any doubt, its not a big deal to file an amended return.
 
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