Learn French: L'apparition avait disparu près du repaire. - The apparition had disappeared near the lair.

It is a common trap! While many verbs of motion or change of state use être, disparaître (to disappear) and its opposite apparaître (to appear) conjugate with avoir in compound tenses. Therefore, the pluperfect form for had disappeared is avait disparu, never était disparu.

I often confuse repaire with repère. What is the difference between them?

Un repaire (spelled with an ai) is a physical hideout, den, or lair, which makes sense for where a mysterious apparition might vanish. Un repère (spelled with an è) is a reference point, marker, or landmark.

Is it intentional that apparition and disparu sound so similar here?

Yes, they share the same linguistic root. Apparition comes from apparaître (to appear), and disparu is the past participle of disparaître (to disappear). Using both in the same sentence creates a deliberate stylistic contrast, essentially saying the appearance had disappeared.