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Apparently she'd been keeping it secret.
Literal
She [topic-は] that [object-を] secret [in-a-state-of-にしていた] [seems-らしい].
~にする with a noun gives 'make X into Y / set X as Y / decide on X' — here 秘密にする means 'make (it) (a) secret / treat (it) as secret.' The ~ていた form locks it into a past resulting state: 'had been keeping it secret.' Adding sentence-final らしい ('seems, apparently, I hear') frames the whole as second-hand knowledge — the speaker isn't claiming first-hand certainty, just relaying or inferring. Distinct from ようだ ('seems like X based on direct observation') and そうだ ('I hear X said' or 'looks X based on appearance'); らしい sits comfortably between hearsay and deduction.