Am I religiously permitted to seize my fraudulent partner's goods to compensate for the money he stole from me in another deal?

If the situation is as you described, then there is no harm in you taking the second merchandise and disposing of it, provided two conditions are met: First, that the selling company of this merchandise is not harmed by it, due to the general saying of the Prophet (peace be upon him): "There should be no harm nor reciprocating harm." Second, that you restrict yourself to taking only what is due to you. If the value of the merchandise exceeds your right, you must return the excess. If it is less, the difference remains your right from him. This is based on the Almighty's saying: "And if you punish [an enemy], punish with an equivalent of that with which you were harmed" and His saying: "And the retribution for an evil act is an evil act equivalent to it." This issue is known as the issue of al-Zafar (taking one's right by force when unable to obtain it otherwise).