Dear XXXXXXXXXX,
Thanks for your question.
It is not too late to amend those returns, and they would not be seen as a negative. It indicates an attempt to comply with the rules.
Schedule C filers are subject to greater scrutiny starting in 2009 because IRS statistics indicate that 65% of under-reporting and abuse of deductions occurs with the schedule C filer.
Generally, the IRS, on audit requires evidence of expenses by use of receipts. Other evidence that meets the condition of a receipt can sometimes be accepted by the agent.
One way to overcome this issue, depends on the type of expense you have. In some cases, especially with major purchases, you can go back the person or business with whom you incurred the receipt, and they may be able to call up an archival copy of the receipt. They may charge a fee for this service. Most businesses will be keeping paid invoices as evidence of revenues and for legal purposes on file in archive or with their accounting, "for as long as the information is required for taxes and legal purposes".
The problem you will have is, that such a move, to amend now, would not generally provide relief from penalties and interest for additional tax due.
Schedule C filers,as a group, oftern do lose receipts, because their record keeping tends to be informal. In my opinon, the auditor would expect to find a few lost receipts. This would most likely result in additional taxes, with interest and penalties to be assessed.
Tax Preparer
GPHR Cert; U.S. Treasury Tax Advocacy Panel appointee