Basically, there are two options, with the first one being the best from your standpoint.
1. Ask for a Corrected 1099 to exclude the loan repayments. (This is the correct way to handle it, as far as the IRS is concerned.)
2. It may be that your family member is reflecting the loan re-payments to you as well as the expenditures made with the original loans as expense on his tax returns, so you may run into some resistance about fixing the 1099s, or it may be a simple bookkeeping mistake made by whomever prepares the 1099s.
If you are unable to get the 1099 corrected, then what I would do is to report the Gross Amount reflected on the 1099 and show the amount that is a return of your loans as a line item reduction on your Schedule C. For example, you could enter the loan repayments on Line 2, Returns & Allowances, which is a subtraction from the Gross Amount on Line 1. If you are filing a paper return, you could enter in the space to the left of Line 2, "Loan repayments included on 1099-MISC in Line 1". If you are filing electronically, the system you are using may not allow that type of explanation; in that case just enter the repayments on Line 2 and if the IRS questions it, you can provide that explanation.
If your family member does not want to or will not correct the 1099-MISC, you may want to point out that when you subtract the repayments from the 1099 figure on your tax return, it is likely that the IRS will question it and you'll have no alternative expect to provide the explanation that the loan repayments were included in the 1099 figure in error by him.
Let me know if you have any follow-up questions.
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Thanks very much,