Your situation can happen.

Let $\mathbb{B}=\text{Add}(\omega_1,1)$ be the forcing to
add a Cohen subset $S\subset \omega_1$, and let
$\mathbb{D}$ be the forcing that first adds such a set $S$,
and then shoots a club through it $C\subset S$. Note that
$\mathbb{B}$ is countably closed in $V$ and therefore
stationary-set preserving, and the generic Cohen set $S$
that is added is both stationary and co-stationary.
Further, the forcing $\mathbb{D}$ is stationary-set
preserving over $V$, because by a bootstrap argument we may
find a dense set of conditions $(s,c)$, where $s\subset
\omega_1$ is bounded and $c\subset s\cup\text{sup}(s)$ is
closed, and the set of such conditions in $\mathbb{D}$ is
countably closed. Thus, $V[S][C]$ is
stationary-set-preserving over $V$, even though it is not
stationary-set-preserving over $V[S]$.

Notice that we may completely embed $\mathbb{B}$ into
$\mathbb{D}$ in the natural way, since $\mathbb{D}$ was
described as first adding $S$, and then shooting a club
through it.

But we may also embed $\mathbb{B}$ into $\mathbb{D}$ in a
different way: by first applying the automorphism of
$\mathbb{B}$ that flips all bits. This automorphism in
effect replaces $S$ with its complement, so that under this
embedding, the club gets added to the complement of $S$.

Thus, if $\tau$ is the name of the generic set $S$ added by
$\mathbb{B}$, then $1_{\mathbb{B}}$ forces that $\tau$ is
stationary, and with the first embedding we have that
$\text{val}(\tau,H_0)=S$, which remains stationary and in
fact containing a club in $V[S][C]$, but with the second
embedding we have $\text{val}(\tau,H_1)=\omega_1\setminus S$, which is non-stationary in $V[S][C]$.

The two embeddings correspond as you said to the two fundamentally different ways we can think about the Cohen set being treated by the club-shooting forcing, since either we shoot the club through the set, or through its complement, and this difference radically affects the stationarity of this set. But meanwhile, all the ground model stationary sets are preserved, since the composition forcing has a countably closed dense set.