So they never go into much detail about the reason behind the dispute other than it was the Federation giving back territory to the Kardasians. No mention of resources other than territory, but what if there was a resource? One never mentioned. Coffee.

"Wait, wouldn't that make Sisko and Janeway opposed to the Federation relinquishing such a vital supply of that oh so good caffine to the no good dirty Kardashians?"

I hear you, and at first I'd agree, but it might be more complicated than that, maybe as an effort to olive branch the relations with Kardasia the Federation decided to let them work the land and market in the area under the conditions of first pick at harvest and discounted rates against common market value, and leaving the rest of the supply for the Kardashians to do as they please and garner trade relations with existing mebers of the Federation and Bajore, and the like.

Why would Kardasia agree? Most likely because the believe themselves superior and can manipulate the contract somehow by subverting the market value. They could raid other suppliers to cause scarcity, or try to redefine market value as the market they create with the surplus.

This would reasonably explain why Janeway was determined to chase Chakotay into the badlands, because that go juice shippment was on hold until an armistice reached, and that replicated stuff, while it dose the job, the real deal hits different.

It would also explain Siskos increasing grumpiness with his morning coffee, he gotta drink literal shit til the good good gets processed through customs.