How exactly does this work? Normally alternate universes are created when someone travels back in time to interfere with history that's already, from the traveler's point of view, happened. When someone changes the course of events in their own present it's not normally called an alternate history - it's just called history. If the Afridhi forge an artifact in the present day that enables them to win a few crucial battles, why would there also be an alternate timeline in which they did not win those battles? When Zugzul gifted the Afridhi with the secrets to creating the Well of Souls, was there also a timeline in which he didn't give them those secrets? Where did the alternate timeline come from? Did Zugzul travel back in time from a future in which the Well of Souls was never made? The module doesn't indicate that, but it'd make more sense if he did.The creation of Zugzul’s Well of Souls has caused a disturbance in the time-space continuum. Throughout the 3,000 years since the event, there are now signs and portents of doom - for the very existence of the artifact is creating an alternate universe in which Blackmoor is conquered by the Afridhi, thus changing the entire course of history.
How did the artifact help the Afridhi conquer Blackmoor? That is, how would the effects of the artifact appear to warriors battling the Afridhi at the time? There's something in the module about the Well "bringing fear to the hearts of the enemies of the Afridhi." Was this a magical fear that caused them to falter in battle? Or does the Well just alter probability so that, effectively, key characters get penalties on their to hit and damage rolls and saving throws? Is a split in the timeline an inevitable result of this kind of tampering with probability, time travel or no? Or were the enemies of the Afridhi simply killed by soul eaters? Why would an artifact whose chief power is creating soul eaters create an alternate timeline instead of just creating a lot of eaten souls?
The PCs seem to have originated in the timeline in which the Afridhi did not succeed in conquering Blackmoor. How would the alternate timeline, if allowed to come to pass, change Mystara's present day? Would the results even be noticeable after thousands of years and a world-changing cataclysm in the interim? Would the Great Rain of Fire have still happened? Might a world in which Blackmoor never ascended to the heights needed to cause a planet-shaking cataclysm arguably be a happier place, even if the price paid was a chunk of one continent dominated by a fire-worshiping tyranny for a time? How, thousands of years later, does one compare the countless souls that would suffer and die or never be born in the Afridhi-dominated timeline to the countless souls who suffer and die and millions more who are never born in the Great Rain of Fire timeline? Why even interfere with that (other than to preserve the party's own existences)?
Has anyone considered playing the module with a party that originated in the Afridhi-dominated timeline, struggling to prevent another party of time travelers from erasing the only world they've ever known?