You have managed to get the clouds moving with a very long exposure, this can bring a fantastic 3D effect to a photo giving the unmoving subject matter so much more presence. Daytime long exposures are usually created with a dark filter to slow down the light. These are called neutral density filters because they are supposed to be neutral and should have no effect on the colour balance. However the very dark filters do tend to alter the white balance and it can be tricky to correct. They also create very high contrast images. It looks like you have encountered those problems here.
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