This has recently come up before. This is my approach. I list every 1099 form on my income tax as revenue (Schedule C). I then list all reimbursements as business deductions (again on Schedule C). The issue of double-counting revenue is a relatively new problem. Again, my approach would be to list the double revenue amounts (once, of course) as a business expense with an explanation. That way, if the IRS ever questions what I did, it would be clear. All 1099 forms would appear on my return so they could match up revenue, and I have taken care of the double-counting in a totally transparent manner.
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