I chose 5 Digi-Egg cards with [Lucemon] in their texts from my trash for this card's [End of Your Turn] effect. At such times, the rules place the Digi-Egg cards at the bottom of the Digi-Egg deck when they would be returned to the deck, but is this effect's "by" condition met?
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Yes, it's met. The conditions will be met even if cards aren't actually placed in that area due to Digi-Egg card or token rules.
Source: EX10-013 Lucemon