Well the best and SAFEST way to remove your skydome fully, is to go to <BULLYROOT>\Config\dat and open default.ide in any notepad.
If you haven't edited it yet, it should look like this:
#
# Resident object definitions
#
##IDE Objects\default.ide
#
#enable plant generator
#
#SHRUB_GEN MODELS\SHRUBS\SHRUBINF.DAT
#skydome
SKY_DOME SKYTOP
SKY_DOME SKYBOT
SKY_DOME SKYOBJS1
#
#enable detail textures
#
DETAIL_TEX
To SAFELY disable the skydome, is to go to this part:
#skydome
SKY_DOME SKYTOP
SKY_DOME SKYBOT
SKY_DOME SKYOBJS1
and safely add a # before all of the SKY_DOME things. So once finished, it should look like this:
#
# Resident object definitions
#
##IDE Objects\default.ide
#
#enable plant generator
#
#SHRUB_GEN MODELS\SHRUBS\SHRUBINF.DAT
#skydome
#SKY_DOME SKYTOP
#SKY_DOME SKYBOT
#SKY_DOME SKYOBJS1
#
#enable detail textures
#
DETAIL_TEX