Le phénomène avait disparu ; toujours est-il qu'il est inexpliqué.

Questions & Answers about Le phénomène avait disparu ; toujours est-il qu'il est inexpliqué.

Why does toujours est-il que take the indicative (est) here instead of the subjunctive?
Even though it ends with que, the phrase toujours est-il que introduces a concrete reality or a factual assertion ("the fact remains that"). Because it states a fact rather than expressing doubt, necessity, or emotion, it must be followed by the indicative mood (il est inexpliqué).
How does toujours est-il que change the tone of this sentence compared to just using mais (but)?
While mais simply contrasts two ideas, toujours est-il que actively pivots the conversation back to the main point after a concession or digression. Here, the speaker admits the phenomenon is gone, but uses this phrase to emphatically say, "Be that as it may, the undeniable fact is..."
Why is disparaître conjugated with avoir (avait disparu) here, when it shows a change of state?
Although many verbs of movement and state change use être in compound tenses, disparaître is a notable exception that takes avoir. So to say "had disappeared" (the plus-que-parfait tense), we must use avait disparu, not était disparu.
Why does the sentence jump from a past tense (avait disparu) to the present tense (est)?
The plus-que-parfait (avait disparu) establishes that the disappearance happened deep in the past. The present tense (est inexpliqué) highlights that the mystery is still unsolved right now. This perfectly matches the function of toujours est-il que, which pulls the focus back to a present, ongoing reality.

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