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No. You calculate the taxable base...which sounds like you say is a loss. After that's you apportion income/loss to the state using a single sales factor (new law change).
The answer depends on whether the NJ activity is part of the same business. Say your S corp is a retail clothing store in NY but also owns 20% of a partnership that owns car washes in NJ. The two businesses are unrelated and you must report the NJ income separately. But if the NJ partnership is a retail store, say hardware, and you invested in it to help your friends and provide advice based on your experience, you can net the two together.
Of course, if this is just one business and you’re tracking profits by customer, you should net them
That's not correct and these are not the facts that OP stated.
In your example (which are not consistent with OP's question), if the partnership and S Corporation are nonunitary, you allocate the partnership income or loss to the S corporation. If the partnership has a net loss and the S Corp (independent of the partnership interest) has positive income, you get to net the loss against the post-apportioned S Corp income.
Whether two pass through entities are unitary or not, you still net everything together at the upper tier level. You flow up apportion for unitary businesses but you allocate for non-untiary. NJ changed the law last year and the 2023 returns now report things this way.
OP's facts are:
1) s corp has profit in NJ.
2) s corp has losses outside NJ.
3) s corp's net income altogether is a net loss.
4) question is whether s corp needs to pay tax in NJ since the NJ only activity is a profit.
5) the answer is no.