No, but that is simply a matter of clicking on the save and using Wrye Bash's "Repair Abomb" feature, so you do not need to worry about that.
http://sites.google.com/site/oblivionpoinfo/stabilization/unofficial-official-patches <-- If you are using OBMM, download the OMOD versions. These should actually be installed before installing FCOM, so when you activate them, choose "no" when prompted to overwrite. If you hold down Shift when you click no, it will not overwrite anything. If Shift does not work, try Alt. Please let me know if you figure out which one is correct.