Ok some things about the timeline are starting to come back to me. The UrSkeks used the crystal in an attempt to purge their evil (Skeksis) half but instead got split into the two beings in what amounted to a celestial transporter accident. The crystal wasn’t cracked until much later, long after the Skekses exiled the UrRu and had taken over the castle for themselves. They had “trials by stone” (called “Haakskeekah”, or something like that), where they proved their worth in “combat” by hitting the crystal as hard as they could. I believe this was a ceremony used to determine who the new emperor would be after the previous one died. The crystal cracked from one of these ceremonies, shooting the shard up and out of the castle. Fearing further destruction of the crystal, they found a “lesser crystal” to perform the same function - the one we saw in the film that the Garthim Master destroyed during a duel with the Chamberlain. So Aughra would not have been around when this happened, explaining why she was shocked to see it damaged in episode 3, when she’s fully in play. That doesn’t explain why she left the Skekses to be the “guardians of the crystal” after evicting the Mystics and clearly not being the most savory of characters. After all, the UrSkeks were trying to purge that half of their being and Aughra knew them before the Sundering. In fact, I believe it was the UrSkeks who built the orrery for Aughra and taught her elevated sight and not the Skekses. I want to let this play out, but it seems that some of the elements explained in the Habidibad were overlooked, or possibly actively ignored.
I think I need to go back and re-read it to see if I’m remembering things correctly, which is not a foregone conclusion, at present.