The eggs are shuffled randomly every time you open the box. There s no way to say which egg is where. The only way to make sure there are no old eggs in the box is to clear them out completely. Empty the box completely on a long walk through the countryside. Save up enough incubators to put all eggs into one, e.g. by saving the last use on any incubators bought. Or save up on 2km-eggs, until there is no 5km-egg remaining.
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Egg sorting
Are the eggs in my bag sorted randomly when I hatch or pick up an egg, or maybe there is a pattern? I feel like sometimes this may cause and egg to stay in my bag forever.