I found only 2 ways of doing it.
Firstly is delete the mob in question.
Secondly is edit the mob in question, and when you get to the screen to edit it's "bio" you can change which group it's afiliated with. this will set it's Base group.
It's important to note you cant remove mobs from thier base group without doing one of the above, but I beleve it is possible to add and remove mobs from groups that is not it's base group using the edit group screen.
I keep a generic Villains group around which I transfer custom mobs I want to remove, as Imoba described.
I have had some interesting effects when some "garbage records" of a mob remained in the custom villain group even after "removal" - caused the costume and stats for a removed EB to be used for an existing minion - so suddendly the mission was swarming with tiny EBs instead of tiny minions...
[url="http://adingworld.wordpress.com/mission-architect-story-arcs/"][b]My Story arcs[/b][/url]: [i]The Siren Supremes[/i] ([b]1143[/b]), [i]The Missing Geneticist[/i] ([b]2542[/b]), [i]Elemental Jones[/i] ([b]263512[/b]), [i]The Soul Hunter[/i] ([b]294431[/b]), [i]Heart of Steel[/i] ([b]407104[/b]), [i]Project Serpens[/i] ([b]434082[/b])
Ok thanks for the advice, now I can cut down on the file size 
Any way to remove custom mobs from a group? So far I can't seem to be able to do it