Affect of brokerage account on my return

Nope.

@carnival- 

Are you using the online or downloaded version ? 

Online

What if I went back to my account and went through the motions of filing an amended return? I have never tried that and I wonder if, once done making changes, the program allows you to cancel the amended return. I know it shows your refund at the top of the screen as you add income, deductions, etc. 

If you use the amendment option then use the downloaded version if possible. When using the online version the "undo amend" will remove the 1040X but it will NOT restore the changes you made which will mess with the archived return.

yes if you want to pay for the desktop version.  then you do your return without brokerage and save use a name like "first return". open again import save as "second return"

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