It depends and it's completely your decision. You would definitely add your explanation to your amended return. The reason you may have been told not to amend is because your tax results won't change. The maximum allowed capital loss for any tax year is $3,000. The tool may not account for the fact that your carryover would be larger.
If you don't amend you will lose the $2,000 loss you believe you should have included. The year that it will make a difference would be in a year when you have large capital gains to offset any losses.
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