I have not tried to mod this game, but this is how (I think) it should work:
I&F has its own session and game files in the "ice_and_fire" folder under "sessions".
Under this folder is the "localization" folder with the "eng_loc_ses_iaf.kfs" file.
Any files common between I&F and WotN (in the "addon" folder) are superseded by the files in the "ice_and_fire" folder for I&F and WotN only uses the files in the "addon" folder, ignoring "ice_and_fire" altogether.
In order to make changes to I&F, all file updates must go into a "mods" folder under "ice_and_fire".
There is one more folder of importance, and that is the "data" folder at the same folder level of "sessions". This folder contains a litany of KFS files with "data.kfs" being the archive that contains the "standard" ATOM's. These are base units like Black Dragons, etc. that are common between TL and WotN / I&F. You can think of them as legacy files.
You can also add a "mods" folder under the "data" folder and both WotN and I&F will use changes to the files in "data.kfs" from files located in that "mods" folder. If you only want changes to affect one game, then they go in the files under the respective "mods" folder for either "addon" or "ice_and_fire".
This is all theory, so try it out and report back your success / failure and we'll try to figure it out!
/C\/C\