The instantaneous duration refers (as it always does) to the spell, not to its effects. This means that the magic of the spell happens in an instant, allowing the spell to produce the effects it says it does. The spell is clear that it has two effects and that they happen in a specific sequence. The caster teleports after which the thunder damage occurs, which is the second effect. The word disappear was used to make it clear that the caster is no longer in the radius of damage when the thunder occurs, but I think it’s an unfortunate choice that creates confusion and that the word teleport could just as easily been used. I also think a different word was chosen for variation and readability.