That is right, it will override any previous shader files that way. Without deleting anything.
I haven't messed with the shaders since, and actually I am not 100% sure again if this does sufficiently change shadow creation. I should do some more tests, but no time for that now.
Before I also tried something with the water shader file, to make the water darker. That one definitely works. Though at long distance it makes the water rather black.
water_simple.frag