I thought I had a similar problem with Merrill Lynch. When I logged into my ML account and look in the tax documents area, I can see two 1099 document files (the original, plus the corrected). After deleting all the ML 1099 forms (B, DIV, INT, MISC) from my TurboTax tax return, I went to import the corrected 1099 into TurboTax Deluxe for Windows desktop. But only one set of 1099s showed up on the import page (and there was no designation to identify which version it was). After importing, the import summary $ values (on the import page) looked the same as the original (uncorrected) 1099. But when I examined each individual 1099 form in my tax return, I found that the numbers all agreed with the corrected 1099s. So after importing make sure you examine each field in each 1099 to verify whether the corrected numbers were imported.
I don't know if the "magic" is implemented by ML or TurboTax, but it seems TurboTax may simply import the most recent (by date) 1099 file?
