This approach is for an arbitrary angle change, and then applied to a $90^\circ$ rotation.
We use the formula for the rotation matrix:
$$\pmatrix{x'\\y'} = \pmatrix{\cos\theta & -\sin\theta \\ \sin\theta & \cos\theta}\pmatrix{x\\y}$$
The vector on the LHS is the new, rotated point; the vector on the RHS is the input point.
For your equation, we have $x=x$, $y=\ln(1+e^x)$. So, we put that in the RHS vector:
$$\pmatrix{x'\\y'} = \pmatrix{\cos\theta & -\sin\theta \\ \sin\theta & \cos\theta}\pmatrix{x\\\ln(1+e^x)}$$
Performing matrix multiplication:
$$\pmatrix{x'\\y'} = \pmatrix{x\cos\theta -\ln(1+e^x)\sin\theta \\ x\sin\theta + \ln(1+e^x)\cos\theta}$$
Now, we insert the desired value for $\theta$, and simplify:
$$\begin{align}
\pmatrix{x'\\y'} &= \pmatrix{x\cos(90^\circ) -\log(1+e^x)\sin(90^\circ) \\ x\sin(90^\circ) + \ln(1+e^x)\cos(90^\circ)}\\
&=\pmatrix{x\cdot0 -\log(1+e^x)\cdot1 \\ x\cdot1 + \ln(1+e^x)\cdot0}\\
&=\pmatrix{-\ln(1+e^x) \\ x}
\end{align}$$
This gives us a set of simultaneous equations to solve:
$$\begin{cases}
x' = -\ln(1+e^x)\\
y' = x
\end{cases}$$
We want to solve for $y'$ in terms of $x'$:
$$x' = -\ln(1+e^{y'})$$
$$-x' = \ln(1+e^{y'})$$
$$e^{-x'} =1+e^{y'}$$
$$e^{y'} = e^{-x'} -1$$
$$y' = \ln(e^{-x'} -1)$$
This process gets the same answer as just switching $y$ and $x$ in the original equation, but it lets us perform other rotations (for example, a $45^\circ$ rotation) instead of just a $90^\circ$ rotation.