After you file

I just added $0.01 to one of the 1099s and that was accepted!

Software should flag this issue prior to transmitting (e-file), and have a way to review and accept as is - by the filer! It's filer's responsibility to ensure it's correct and IRS will match up anyway with what 1099 issuer submitted.

These 2 1099s have different Account numbers in the form when I look at all the detail, so they should never have been flagged as duplicates to begin with.