Do the files replace core files? if not, they will be safe even if they are in core folders. Are they in folders that have overrides available?

V1.3.9 will only have bug/security fixes for v1.3.8a, so it shouldn't be hard to merge any files as long as you keep good records of what you have. V2.0 will require all mods to be rebuilt anyway, so the structure of this mod will become irrelevant.