We can prove this without using Parikh's theorem. Assume that a language $L$ over the two-letter alphabet $\{0,1\}$ is given by a finite-state machine. For the language $\mathrm{SCRAMBLE}(L)$ we construct an automaton with one register capable of holding any integer (positive or negative). The states are the same as in the finite-state machine. Transitions that read $1$s are simply copied to the automaton. Transitions that read $0$s are replaced by transitions that decrease the register. In addition, at each state we add a loop transition that reads a $0$ from the input tape and increases the register. This one-register automaton accepts the language $\mathrm{SCRAMBLE}(L)$ if we require the register to contain zero at the end. Indeed, let $w \in L$ and $t \in \mathrm{SCRAMBLE}(w)$. In order to accept the word $t$, our non-deterministic automaton guesses the word $w$ and follows the same sequence of states as the original finite-state machine that reads $w$. During this process the integer register keeps track of surplus $0$s seen in the word $t$ (this number can be negative).
Finally, we convert this automaton with one integer register to an ordinary pushdown automaton with two stack symbols, one of them used for representing positive values of the register, the other one for negative values. These two stack symbols are $A$ and $B$; they play the same role as the stack symbols "zero" and "negative zero" in Yuval Filmus's answer. We require the stack to be empty at the end. It can be shown that this pushdown automaton recognizes the language $\mathrm{SCRAMBLE}(L)$.
A direct formal construction follows. Here we skip the intermediate step with the one-register automaton and go straight to the final PDA. We are going to use the definition of a PDA without initial stack symbol and with the following acceptance mode: an input string is accepted at a configuration if the complete input string has been read, the stack is empty, and the PDA is in one of its accepting states.
Suppose $L$ is recognized by a non-deterministic finite automaton, which is a tuple $M=(Q,\Sigma,\delta,q_0,F)$, where $Q$ is a finite set, $\Sigma = \{0,1\}$, $\delta$ is a function from $Q \times \Sigma$ to $\mathcal{P}(Q)$, $q_0 \in Q$, and $F \subseteq Q$. If we follow the above construction, then for $\mathrm{SCRAMBLE}(L)$ we obtain the PDA $M'=(Q,\Sigma,\Gamma,\delta',q_0,F)$, where $\Gamma = \{A,B\}$ and
\begin{align*}
\delta'={}&\{(p,\epsilon,\epsilon,q,\epsilon) \mid q \in \delta(p,\epsilon)\}\\
&\cup\{(p,1,\epsilon,q,\epsilon) \mid q \in \delta(p,1)\}\\
&\cup\{(p,\epsilon,A,q,\epsilon) \mid q \in \delta(p,0)\}\\
&\cup\{(p,\epsilon,\epsilon,q,B) \mid q \in \delta(p,0)\}\\
&\cup\{(p,0,B,p,\epsilon) \mid p \in Q\}\\
&\cup\{(p,0,\epsilon,p,A) \mid p \in Q\}.
\end{align*}
We define a function $\mathrm{unary}:\mathbb{Z}\to\Gamma^*$ by putting $\mathrm{unary}(n)=A^n$ for non-negative $n$ and $\mathrm{unary}(n)=B^{-n}$ for negative $n$. For example, $\mathrm{unary}(2)=AA$ and $\mathrm{unary}(-2)=BB$. One can prove that if $|w|_1=|t|_1$ and $(q_0,w)\vdash_M^*(q,\epsilon)$, then $(q_0,t,\epsilon)\vdash_{M'}^*(q,\epsilon,\mathrm{unary}(|t|_0-|w|_0))$. (We use induction on the number of steps plus $|t|_0$.) Thus, if $M$ accepts $w$, $|w|_1=|t|_1$, and $|w|_0=|t|_0$, then $M'$ accepts $t$.
On the other hand, by induction on the number of steps one can prove that if $(q_0,t,\epsilon)\vdash_{M'}^*(q,\epsilon,\gamma)$, then there exists a word $w$ such that $|w|_1=|t|_1$, $|t|_0-|w|_0 = |\gamma|_A-|\gamma|_B$, and $(q_0,w)\vdash_M^*(q,\epsilon)$. Thus, if $M'$ accepts $t$, then $M$ accepts $w$ for some $w$ satisfying $|w|_1=|t|_1$ and $|w|_0=|t|_0$.