。
It seems she knew the truth of the matter.
Literal
She [topic-は] matter [possessive-の] truth [object-を] was-knowing [seems-ようである].
事 (こと) here is the abstract 'matter, affair, business' — 事の真相 ('truth of the matter') is a near-fixed phrase suggesting hidden depths to a situation. ~ようである is a formal/literary equivalent of ~ようだ ('seems, appears') — the same evidential, just with the formal copula である instead of plain だ. Common in newspaper writing, formal essays, and reflective narrative. 知っていた (resultative ~ていた past) marks knowing as a past state, not a moment of learning.