That is because the Awoken didn't exist until after the Collapse. The Marasenna and Awoken of the Reef lore books basically cover the history of the Awoken. They're definitely worth reading but here's the basic summary: The Awoken were once normal humans, about 900 crew and 40,000 passengers aboard the Exodus Green, who were leaving Sol to start a new space colony elsewhere. These humans included a major characters such as Mara, Uldren, Osana (their mother), Captain Alice Li, etc.... When the Collapse happened, Darkness and Light collided in space and created a paracausal singularity which pulled the Exodus Green into it. Mara was the first to physically incarnate within the singularity, and her chosen form defined what the Awoken could be. From there the Awoken would develop a utopian society on their new home-world within the singularity which they called the Distributary. Time within the Distributary passes faster than time outside it, so the few centuries that passed for Sol was the equivalent of several thousand years within Distributary. Mara spent her time studying the Distributary, space, building her space fleet, and playing politics in an effort to rally those who would return to Sol. Eventually Mara's efforts would succeed and she would lead tens of thousands of Awoken out of the Distributary and back to Sol. When they returned several centuries had passed since the Collapse, and they began to terraform and settle the Reef. Once the Awoken discovered what had become of Humanity, some Awoken wished to return to Earth and provide what assistance they could, while others wanted to remain hidden in the Reef for their own safety. This led to riot and ultimately Mara allowed those who wished to leave to for Earth to do so on the condition they were not to return. The Awoken returned to Earth became known as the Earthborn those who stayed in the Reef became known as the Reefborn. So yeah... the Awoken were never around to encounter or endure Clovis and his experiments. As far the Awoken were concerned prior to their return to Sol, Clovis Bray was basically a legend/myth or just a scary bedtime story for little children.

There were no awoken during the golden age. They were created during the collapse.