This isn't a mod issue, but rather a problem with the game's resources (or the developers intentionally broke something). Proof: the death animation model still exists in the game's resources, and I've attached it to regular ents, and they also disappear. I think the only way to fix this bug is to make ents an NCF creature and replace them in the ent upgrade tree.
A complete lineup of such a creature has existed for a long time!
As for the disappearance, that's a copyright issue...

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Неудачное планирование ведёт к неудаче ...
NCF - мод, добавляющий дополнительных существ в HeroesV 3.1