I do not think anyone ever claimed we could recover DNA from Paleozoic trilobites
Evolutionary theory rests on a foundation of multiple lines of evidence, including fossil record, comparative anatomy, biogegraphic distribution, genetics, laboratory experiments.
Genetics pointing to evolutionary divergence is best suited to modern and geologically recent genera.
Other lines of evidence come into play for the remote past. At least that is my understanding, I am not formally trained in the life sciences
As with any theory, there are uncertainties, and things we do not know.
The mere existence of uncertainties however does not constitute evidence of the hand of divine providence