I have done this multiple times, and I know that the experience is applied appropriately. I kept count of the amount of Pokémon I evolved and how many did/did not gain the XP bonus.
This experiment was carried out by not exiting the menus until I had completed the evolutions, as well as timing the applicable duration of the XP boost. Additionally, all of these Pokémon (and their evolutions) had already been added to the Pokédex, so no additional bonuses were gathered (however, from additional testing this is also appropriately applied).
Pokémon evolved under the effects of the Lucky Egg:
- 12 Pidgeys
- 4 Rattatas
- 2 Zubats
- 1 Oddish
- 1 Paras
- 1 Caterpie
- 2 Weedles
- 1 Slowpoke
Total XP: 24000 (1000 XP per Pokémon)
After 35 mins (to make sure that the effect had ended) of applying the Lucky Egg - Pokémon evolved without the Lucky Egg
- 2 Pidgeys
- 1 Rattata
- 1 Psyduck
- 1 Goldeen
Total XP: 2500 (500 XP per Pokémon)
Upon exiting to the map, I levelled up, and was greeted with a counter of 26500 XP.