Makes sense.
I can't account for why they used NSF or stop pay on the claim form, but you're right that there is no point in redepositing if it was stop pay in the first place. Stores routinely redeposit because over 47% of bounced checks clear on the second go-round
If it was NSF when issued and first bounced, there would be time to get a stop order in place by the time of redeposit.
I haven't lived in Canada in many years and had no reason to know the check laws when I did. But, when states started creating laws to impose civil damages for bounced checks, almost all of them only covered NSF and A/C checks. It was thought that a stop order actually indicated a valid dispute.
But check kiters saw the loophole before politicians and, when it was known or belived that a check would be NSF, they placed a stop order to avoid damages. Later, the laws were amended to cover stop orders, "if a valid dispute could not be shown".
What that history lesson means is that, whether the check was not covered by good funds when issued or whether negotiation was prevented without good cause now is a distinction without a difference. On the facts of your post, if your boss can't establish a valid dispute, justifying a stop order, you should end up liable to moneymart (because you cashed the check and got paid by them) and your boss should end up liable to you (because of the worthless instrument).
Good luck.