No, it doesn’t activate. [EX5-070 X Antibody Proto Form]'s inherited effect will trigger/activate "when this Digimon would leave the battle area other than by one of your effects," but since [EX5-070 X Antibody Proto Form] isn't in this Digimon's digivolution cards at the time of activation of the [On Deletion] effect because it's placed in your security stack before this Digimon is deleted, the "if [X Antibody] was in this Digimon's digivolution cards" condition isn't met, so the effect doesn't activate.