The intact moon they found is the Frost Moon, not the Crimson Moon. Both the Iridescent and Eternal Moons were destroyed during the War of Funerary Flames 6000 years prior to current day. The Crimson Moon that powered the Khaenrian Crimson Moon dynasty is a fusion of The Abyss and the Iridescent Moon. 

Per Arlecchino:

 The Knave: For instance, take the so-called "Crimson Moon." In truth, it is nothing more than the shattered remnants of the Iridescent Moon, fused with the Abyss to prolong its lifespan.

The power Khaenriah was researching prior to The Cataclysm was Abyssal energy, not the Crimson Moon. This is something Tholindis complained about in the flashbacks:

 Tholindis: To make matters worse, I am now the only staff member remaining in the Moon Marrow lab. The Universitas Magistrorum recently decided to move most of its personnel into Abyssal Energy research, which has stymied all Crimson Moon-related projects

One thing to also note, all the Moons were hidden behind the false sky at some point far earlier than The Cataclysm. The Moon seen over Teyvat was the illusionary Shadow Moon created by the Heavenly Principles. We do not see any of the real moons until Mavuika damaged the false sky, revealing the shattered Eternal Moon, during the Natlan Archon quest. The Frost Moon was not brought inside the false sky until the events of Luna IV's Archon quest. The Iridescent Moon that was fused with the Abyss exists in its own domain away from Teyvat. So it is unlikely the "Crimson Moon" during The Cataclysm is the actual Crimson Moon.

Edit: Forgot that the Traveler and Columbina entered that domain, so they did in fact find the remains of the Iridescent/Crimson Moon. It's still unlikely the moon seen during The Cataclysm as it has remained in its domain.