The collapse of Arc-Nyx is resulted from the increasing instability within the structures of Spacetime between Arc and Nyx universes. This is due to the repeated ripping of spacetime, producing unstable wormholes (instead of structurally supported portals) between Arc and Nyx.
Think of the supporting structures between Arc and Nyx as pillars. Any unstructured opening of spacetime will cause these pillars to break. If enough of them break, it may result in a chain reaction which causes the universe to shatter or collide with another.
The first instance of this instability in spacetime was created by Magnya Ullisca, who sliced and ripped open the fabric of spacetime, which buckled under its own weight and subsequently created a major explosion in both Arc and Nyx. Subsequent opening of spacetime by Nyx divinities (from exiling Nyx humans to Arc) and other tears in spacetime caused the pillars keeping Arc-Nyx apart to weaken. The breaking point was nearing the end of the battle of Nyx Planet, when Slash, combined with the core powers of the Core of Spacetime, Awakening, Life and Death, sliced open spacetime again to defeat Guinevere and Aeolus.
Arc and Nyx collide together, breaking off many pocket universes “chunks”, which pulled a lot of weight off of Catalana.
After Catalana was defeated, Cassandra Fusallo completed the merger of Arc-Nyx, removing many of the small pocket universal debris.
Cassandra Fusallo’s direct tampering with what enters the final state of ArcNyx was due to the fact that she was satisfied with her original experimentation premise, and that she considered it the end of her Butterfly Effect experiment by the time humanity reached the modern era (~1900s) in Arc and Nyx. However, as she wanted to leave Arc-Nyx alone, the discovery of Nyx’s divinities discovering they could send/exile humans to Arc began weakening the support structures.
The eventual collapse of Arc-Nyx turned from a completed experiment into a post-experimental disaster. Her subsequent cleanup was to deal with the mess and eventually leave ArcNyx to exist and develop as a normal universe.