Control even managed to invade the body of former Section 31 head Leland, so there’s really no telling where and when it could resurface in Season 3.
Control was defeated in Season 2, but it’s worth mentioning that Control didn’t seem to be one individual entity.
Control definitely seemed like a big bad who would resurface in Star Trek: Discovery, but we can only see if it’ll be able to track down the crew and get control of the data so that it can destroy all organic life.
Its possible Control exists in many different forms and can survive in just about any setting where there is an electronic basis for it to inhabit.