From the beginning I've noticed a discrepancy between people claiming that fairies in Eureka disappear after a short time and my personal experience as a Ninja sneaking my way into lv20 area and always finding the same Fairy after hours.

At first I thought the fairies in higher level areas behaved differently, that they lasted longer than those found in lower level zones. But then today I noticed how quickly a fairy in the Ziz camp disappeared after the FATE train passed, even though I've seen a fairy staying there for more than a hour in the past.

So my current theory is that fairies are like soap, the more you use them the more you consume them, and when you use them too much they disappear into nothingness.

Basically Fairies do not disappear after a certain time but after a certain amount of times they have given their buff.

This theory is also supported by the fact fairies do not cast their AOE if you already have the buff, even if it's 2 mins from expiring. Likely this was a measure taken to avoid a single person making a fairy disappear.