Is Zakat obligatory on merchandise that has been stagnant for three years, while its owner owes his partner debts equal to or exceeding the value of this merchandise?

If you have surplus money beyond your needs, you can use it to offset the debt. Deduct the amount of the debt from the value of the goods. If a nisab (definition) (minimum taxable amount) remains, zakat (definition) is obligatory; otherwise, it is not, because debt nullifies zakat on trade goods. Continue to pay zakat on trade goods by appraising the merchandise when a year has passed on the original capital and paying a quarter of a tenth (2.5%) of its value.