If your financial institution revises your 1099 information, you should expect the download of the revised information to override the information that is in your tax return today. Any detailed updating of this information that was done by hand will be lost.
If you are using a Desktop version, you have the option of saving a copy of today's tax return. Then, you would be able to compare the first version with the revised version to see how material the changes were to your income tax return. Or retrieve the original version and start over again should the need arise.
These options are not available using the Online versions.
I would compare the original paper copies to the revised paper copies to get a sense of the magnitude of the changes that I should expect to see. Then I would use the method of handling the revisions that make the most sense to me in managing my tax data.
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