If it is only those files then the reason is clear: the changes you make in EDA and EDCT do not 'make it into the game' because the text is not automatically updated (the game effects will 'make it', regardless of the text).
You need to change the relevant entries in the corresponding text files as well:
EDA:
Code:
Ancillary accomplice
Type Security
Transferable 0
Image sex_yangman.tga
ExcludeCultures mesoamerican
Description accomplice_desc
EffectsDescription accomplice_effects_desc
Effect Subterfuge 1
EDCT:
Code:
Trait GoodCommander
Characters family
AntiTraits BadCommander
Level Promising_Commander
Description Promising_Commander_desc
EffectsDescription Promising_Commander_effects_desc
GainMessage Promising_Commander_gain_desc
LoseMessage Promising_Commander_lose_desc
Threshold 1
Effect Command 1
EDA --> text\export_ancillaries
{accomplice_effects_desc}+1 to agent's skill
EDCT --> text\export_vnvs
{Promising_Commander_effects_desc}+1 Command