mm ok, but how do i edit what to skip when using that? or does the latest version automatically skips those files which may cause problems (i've read about those egm files whatever they are).
egm files are like face related (helmets and such) and anyway yes there is like an oblivion related ini like thing that has all the files it needs to skip. Most, if not all the kinks have been worked out and you don't have to worry about it.
But follow the recommended method - first place the meshes you want to optimize in the in folder run the PyFFI with the right click on the ini file thingy then in the resulting out folder will be the optimized meshes MINUS what was not supposed to be optimized - so you then copy the meshes either back into the in folder and rezip the BSA from there or if you have the backed up meshes elsewhere then copy the optimized ones back in over those. This way you will overwrite the non-optimized meshes and keep the ones that were skipped anyway.
Regarding Game breakeage-
Well I would not have ever just torn into running the PyFFI on the loose meshes - anything I do is backed up.
If you back everything up and then install everything with an installer - http://www.gamesas.com/index.php?/topic/1084204-bain-mod-installation-projects/ - then you should be fine because if you make a mistake then it is just a matter of replacing the files again.