Seems odd the latest update would break those files, I mean they aren't even originally part of the update data so it should still just be trying to overwrite them on the base game, taking a quick look at the files with the .arc files extracted the only difference seems to be some .mca (audio) files and the .cro files, I've no idea what a .cro file does, I believe Pokemon has them also? imagine the code.bin also changed.
I can't imagine anyone is really going to look into it much with MHG and MHXX around the corner.
At the very least maybe you could rebuild the base game with the patch? was how it originally worked till the update came along and was easier to contain the english patch within that.