It seems to me that the easy way to do this is to solve your replacement 
for `x`:

cos(4*x+6).subs(x, (u-3)/2)

And if this is just a special case of a more general substitution, you can 
of course do that solve step with sympy.

I can't tell from your question, but this might not be exactly what you 
wanted.  For example, look at

(x*cos(4*x+6)).subs(x, (u-3)/2)

This will also replace the `x` out front.  If you don't want that, you'd 
need to do an even more complicated version of what Francesco suggests.

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