Small businesses, of course, often find it easier to maintain all electronic records --- financial statements, client lists, sales data and the like --- within a single application. "The new software is very comprehensive," says Giovanni Coratolo, vice president of small business policy with the U.S. Chamber of Commerce. And as a result, small businesses often have proprietary, non-tax data contained within the files it would provide during an audit. So they risk providing the IRS with information that's outside the audit scope.

The concerns date back to about mid-2009, when the IRS began training its agents on the use of QuickBooks accounting software, says Benson Goldstein, the AICPA's senior technical manager, taxation. Once they gained proficiency, agents could conduct exams directly within the application. And some began asking for the electronic files, he notes. And at least a few tax professionals instead turned over printouts of the information. Based on Goldstein's conversations with different accountants, some IRS agents accepted the paper documents. Others didn't.

The AICPA grew concerned that some business owners could be compelled to submit more information than necessary, Goldstein says. "There's certain data," he adds, "that should be private."

What's more, by turning over information covering multiple years, businesses risk having to defend actions going back five or ten years, says Coratolo. "That's problematic when you have limited time and resources."