While business losses are never a positive benefit, appropriate planning for the utilization of the loss is important. When you sustain a business loss, it means you have spent more money than you started with. In order to have spent that excess, it had to come from somewhere. In order to continue in business, you're going to have to replenish that source. How you replenish that source will have tax implications.
To create the loss, you had to have spent the money from previously accumulated earnings, borrowed funds and/or original capital.
Each one of these is a scarce resource in an ongoing business venture. In order to restore these amounts in the future, the company will have to generate taxable income. If you utilize the current loss to offset a Roth IRA conversion, you'll have to work doubly hard to pay the taxes on these future profits. This may be the flaw in your thinking.
Rather than use the loss for the conversion, you can elect to carry forward a business loss to future tax years. By electing to carry forward the loss, you can mitigate the future tax impact of profits. Alternatively, if you need some capital, you can carry back your loss to prior year's taxes and get a tax refund. A $100,000 loss carried back to a prior tax year may generate up to a $35,000 refund if you were in high tax brackets previously.
Before you worry about the SEP IRA, I would worry about the future needs of the business.
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