You love replying to my threads huh? Haha.
This part made be confused.
'The radius needs to be sufficiently set to be outside the farthest from where the command the ran (ie: a base at 100,100, ran at 0,0, needs radius of 100 at least to make sure part of it gets in, 150 would probably get most of their base...etc)'
I understand the border would need to be a good size outward from the base that is the most farthest from the center point so it doesn't delete their base. Whether this is what you meant, I don't know.
Update: I ran the trim command, looks like it's too much work for dynmap to auto update so I have to do a fullrender. How easy is MCedit to use? I recall using it once and it was insanely difficult since I'd have masses of land to delete in between bases etc.
Will extra biomes then render properly?