It applies to them because the game uses a similar logic for loading .txt-s.
If two .txt-s contain the same skill, stat block, crafting combination, etc. one of them will overwrite the other.
The proper way to prevent this is to remove stuff from the .txt that you didn't actually modify.
eg. if you only changed the Fortify ability, you should remove *everything* from your SkillData.txt except the following:
new entry "Target_Fortify"
...
new entry "Target_Fortify_3"
...
data "Level" "3"
This way it won't overwrite someone elses stuff.
