The De minimis safe harbor election is determined per invoice item. If the cost exceeds $2,500 per invoice (or item), no part of the cost may be deducted by using the de minimis safe harbor. If you have an applicable financial statement, then you may increase the per item or per invoice amount up to $5,000.
In the example you have given you would not be able to use the safe harbor as the invoice cost for the new AC + furnace exceeded $5000. If the invoice amount is within the limits allowed then you are correct that each co-owner would receive a percentage.
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