I recently had to change my caulk box around the map and now when i compile above ground looks like this http://prntscr.com/4dhvc8

Dynamic sunlight is working on only models and its disregarding brushes / terrain patches.. I thought it may be because i havnt textured the inside faces of the caulk box but i also found that my "sky" textures magically dissapeared.

Any ideas will be appreciated, thanks.

Make the inside faces of the caulk box a sky texture. It doesn't matter which sky texture. It just needs to be a sky texture. That's all I can think of. It doesn't disappear you just can't see it when there is a skybox model.
Maybe add your skybox and worldspawn settings again
http://wiki.modsrepository.com/index.php?title=Call_of_Duty_5:_Skybox
http://wiki.modsrepository.com/index.php?title=Call_of_Duty_5:_Worldspawn_Settings