That is we have a linear transformation, i.e. an $ n\times n $ matrix $A$, such that for every pair of vectors $ v $ and $ w $ we have
$$ \langle v,w\rangle=0 \ \ \ \implies \ \ \ \ \ \langle Av,Aw \rangle = 0 $$
What are all such matrices?
I've got this solution: [The idea is to first prove that such a matrix is necessarily angle preserving, from which then by Angle preserving linear maps we get the answer.] If $A$ is not invertible, then the question is invalid, technically, so we deal with invertible maps only. Take any two vectors, and use Gram-Schmidt to orthoganalize them $$ z:=v- \frac{\langle v,w\rangle}{\langle w,w\rangle} \ w \implies \ \langle z,w\rangle=0.$$ -- which can be confirmed by directly writing out their dot product.
So, by assumption $$ \langle Az,Aw\rangle = 0 $$ Writing out: $$ 0= \langle Az,Aw\rangle \implies \langle Av,Aw\rangle=\frac{\langle v,w\rangle}{\langle w,w\rangle} \langle Aw,Aw\rangle $$
But this holds for any two vectors, in particular when you exchange roles of $v$ and $w$: So for any two $v, w $ $$ \langle Av,Aw\rangle=\frac{\langle v,w\rangle}{\langle w,w\rangle} \langle Aw,Aw\rangle =\frac{\langle w,v\rangle}{\langle v,v\rangle} \langle Av,Av\rangle \tag{$*$}$$
In the middle equality, divide (we will see that at the end the equality we want holds, even when $\langle v,w\rangle=0$, so this is safe!) to get $$ \frac{\langle Aw,Aw\rangle}{\langle w,w\rangle} = \frac{\langle Av,Av\rangle}{\langle v,v\rangle} $$ From which we get $$ \frac{\langle Aw,Aw\rangle}{\langle w,w\rangle}=\frac{\sqrt{\langle Aw,Aw\rangle}}{\sqrt{\langle w,w\rangle}}\frac{\sqrt{\langle Av,Av\rangle}}{\sqrt{\langle v,v\rangle}} .$$
Now replace in the middle equality of $(*)$ and rearrange to get $$ \frac{\langle Av,Aw\rangle}{\sqrt{\langle Aw,Aw\rangle}\sqrt{\langle Av,Av\rangle}}=\frac{\langle v,w\rangle}{\sqrt{\langle w,w\rangle}\sqrt{\langle v,v\rangle}} .$$
But see the denominators:
$$ \frac{\langle Av,Aw\rangle}{\|Aw\|\|Av\|}=\frac{\langle v,w\rangle}{{\|w\|\|v\|}} \tag{$**$}$$
Notice that the division above was safe, since for orthogonal pairs this already holds from the hypothesis.
But $(**)$ just means that the map $A$ is angle preserving (not just right angle preserving!)
Now see the beautiful proof in the link above that all and the only angle preserving maps are (nonzero) multiples of an orthogonal matrix.