You are an investor. So the business operates as though you had made no loans. The only thing that shows that they received money from you are transactions on their balance sheet. Your loan is not income to them - it just increases their operating capital. So all the expenses that they pay are still deductions.
When you're looking at the balance sheet of this company there should be a credit for the money that you gave them (either as cash in the bank or assets that they purchased) as well as an offsetting amount in the 'long term liabilities' section. That long term liability is the amount that they owe you. When they give you back your money it isn't a taxable event - it's just a return of the money that you gave them. But if they pay you any interest - and I hope you are charging them interest - then you will declare the interest earned as income on your tax return and they will declare the interest that they paid you as an expense on their tax return.
@Texasbbs
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