Hi there!
This is not related to the “import local mods” problem that was addressed last month.
However, the error message describes what you should do.
Touching the data file with AGE is not necessary if you do not want to update it, and you only need to add a “civilizations.json” file next to the dat file in your data mod folder (you can copy it from the base game). Then you will need to open and edit the json to remove three new civilizations from the bottom, so that only 45 civs are expected to be loaded by the game when your mod is on.
Always add the civilizations.json file to every data mod you make. This will ensure that it keeps working whenever the base civ pool gets an update.
This is not recommended. Adding placeholders in the data file makes it possible for those civilizations to be selected with the Random Civ option, which would crash the game.