Solved but I will keep it here because it may help someone else. The problem is that a folder is missing in the path.
It is NOT /Game/Mods/Brachiosaurus for example, but instead:
/Game/Mods/Additions_Pack/Brachiosaurus
This fixes it.
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Hello there :)

I use the Super Structures/SS mod and I have edited the pull lists to have all unfertilized eggs in the game. This means that I can put all unfertilized eggs into their own dedicated storage boxes and keep things nice and organized.

There is a weird issue with the Acrocanthosaurus Egg and the Brachio Egg, however. The dinos lay the eggs just fine, but I cannot put them into the Dedis I made for them. If I go to the wiki however and I copy the spawn command for the eggs and cheat in an egg, I CAN put that in the dedicated storage (because the blueprint is obviously the same, as this is what I put into the custom pull list as blueprint).

So all I can think of is that the blueprints on the wiki for both of these eggs are NOT the same as the ones for the eggs the creatures actually lay (also the wiki has no fertilized egg codes listed so this is suspicious).
In other words, I need (slightly?) different blueprints. Does anyone know them?

These are the ones I use:
/Game/Mods/Acrocanthosaurus/Blueprints/PrimalItemConsumable_Egg_Acro.PrimalItemConsumable_Egg_Acro

/Game/Mods/Brachiosaurus/Blueprints/PrimalItemConsumable_Egg_Brachiosaurus.PrimalItemConsumable_Egg_Brachiosaurus

The issue may exist with (some) of the other creatures too, but I don't have those eggs yet.