@tomw @loke
In normal use I would say you'd use "dag" ("jag är på resa i fem dagar" - I'm traveling for five days), and only use dygn when either there's a risk of confusion or you want to emphasize the 24-hour span for some reason.
So with "han har varit försvunnen i tre dygn" (he's been missing for three days) it emphasizes the time span and the seriousness of the situation.