、。
It just so happened that she had taken that day off.
Literal
She [topic-は], by-chance that-day [topic-は] day-off [object-を] [had-taken-とっていた].
The doubled は — once on 彼女, again on その日 — sets up a contrastive layered topic: 'as for her, regarding that particular day...' Japanese accepts multiple は-marked elements in a sentence, with each setting a different scope. The comma after 彼女は is a stylistic pause that emphasizes the layered topic structure rather than a grammatical break. 休みをとる ('take time off') is the standard collocation for taking leave from work; とっていた combines the te-form with the past resulting-state ~ていた, giving 'had (already) taken' — the day off was a fait accompli when whatever happened occurred.