We saw her transform as a child, so does that mean there have been other instances in the past where Killer Frost has taken over and Caitlin wasn’t aware?
Season 5 showed that Frost can go dormant for long stretches of time, so it’s possible she could’ve emerged without Caitlin being suspicious of her existence before she officially learned about her.
As far as how that will go down we can only speculate, as there’s a lot of unanswered questions about Caitlin and Killer Frost’s co-existence.