Hey we had the same issue this worked for us "NPCReplacements=(FromClassName="Gigant_Character_BP_C",ToClassName="")" that is for the normal gigas, but there are also mod gigas, you need also this one "NPCReplacements=(FromClassName="Gigant_Character_BP_Core_C",ToClassName="")" and of course when you ingame do a wild dino wipe "admincheat destroywilddinos"

yeah tried that didn't seem to fix it.. overall unfortunatly we choose to remove extinctioncore

Yeah, not much you can do when the mod creator hasn't updated the mod in years. Best of luck on your next dino mod!

If you use this code in your Game.ini the problem should be solved:
ConfigSubtractNPCSpawnEntriesContainer=(NPCSpawnEntriesContainerClassString="CI_DinoSpawnEntries_BoneGiga_C",NPCSpawnEntries=((NPCsToSpawnStrings=("Gigant_Character_BP_C")),(NPCsToSpawnStrings=("Gigant_Character_BP_Core_C")),(NPCsToSpawnStrings=("Liquefied_Gigant_Character_BP_C"))),NPCSpawnLimits=((NPCClassString="Gigant_Character_BP_C"),(NPCClassString="Gigant_Character_BP_Core_C"),(NPCClassString="Liquefied_Gigant_Character_BP_C")))

It removes every giga spawn from eldritch isle without completely removing them from the map. The spawn entry "CI_DinoSpawnEntries_BoneGiga_C" seems to be broken with extinction core. I searched a little bit through the files. I also use a spawn entry to add them to the isle again without overspawning:
ConfigAddNPCSpawnEntriesContainer=(NPCSpawnEntriesContainerClassString="CI_DinoSpawnEntries_BoneDinos_C",NPCSpawnEntries=((AnEntryName="GigaSpawner", EntryWeight=0.1, NPCsToSpawnStrings=("Liquefied_Gigant_Character_BP_C"))),NPCSpawnLimits=((NPCClassString="Liquefied_Gigant_Character_BP_C", MaxPercentageOfDesiredNumToAllow=0.00075)))