It may help to try the upload from a different browser or to clear cache and cookies and try again. This can resolve problems on many different websites. This TurboTax Help article has directions.
If the IRS has a contact phone number in the letter, you can try calling them to resolve the difficulty with the upload.
Or, there should be a fax number listed in the letter to route the documentation to the correct department which is doing the research.
Or, there should also be a mailing address that will route it to the correct department.
If you do fax or mail, I suggest you send them a copy of the letter they sent to you, for reference. And if you mail it, I would send it with tracking, so you can show that it arrived safely.
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