By the end of Justice League, Silas and Victor seemed be on better terms, and Silas was shown helping Victor further explore his cybernetic abilities, which included redesigning his body.
Just like in the comics, Silas rebuilt Victor’s damaged body after a car crash nearly killed him, only in the DCEU, Victor’s robotic body was assembled by one of the three Mother Boxes left on Earth.
This led to various story changes, though Silas Stone being kept alive is certainly one of the tamer alterations.
When Steppenwolf arrived on Earth, Silas and other S.T.A.R. Labs scientists were taken because they’d been in contact with the Mother Box, but Cyborg, Batman, Wonder Woman and Flash managed to get Silas and the other survivors away.