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What you are asking is a little contradictory in that you want to completely replace the sketched colors by brushing but you want to retain brush transparency.
However this may work for you.
Put your layers in the order show below:
At the bottom is a plain white layer
Next is an empty layer for the new shading
On top of that is the guide shading which you want to replace. This layer has the "blend if" set to blend if the layer below is white
At the top is the illustration drawn in black on white. This top layer is set to multiply blending mode
Blend if for old sketch layer :
Before drawing on the "new shading layer it looks like this. The black and white is on the top layer the colours on the old guide layer.
If I paint with anything but pure white on the New shading layer - it replaces what is on the old shading layer. The brush opacity allows new colors to be mixed but does not show the original sketched shading .
It does leave a border on the old guide color around soft brushes but when finished just switch the old guide layer off.
Hopefully that will get you started
Wow this is great, pretty much what I've been looking for almost to a T
Is there also a way to to keep the destination layer covered by the layers over it? Like if that background layer had something drawn on it, would I be able to make the old guide shading and new shading layers show on top of it?
To bring back the old guide shading - change the blend if back to 0-255 (by sliding the black triangle back to the left*) and reduce the opacity. You could also try different blend modes to give a different mix.
* When adjusting "blend if" sliders you can also hold down the Alt key and the slider triangle will split allowing you to create a gradual transition between the two split layers