Are you referring to files in the config\spacecraft? also, do you mean to delete the whole thing, eg:
[DOCK_0]
;to shuttle
POS=(0,0.625,1.082)
DIR=(0,0,-1)
ROT=(0,1,0)
DOCK_1]
;to node
POS=(0.00,-0.086,-1.278)
DIR=(0,0,1)
ROT=(0,1,0)
I had a problem of my rectangles appearing at the back...