$\newcommand\R{\mathbb R}\newcommand\C{\mathbb C}$No, there is no uniqueness here.
Indeed, let $\hat f$ denote the Fourier transform of a (say integrable) function $f\colon\R\to\C$, so that $\hat f(t)=\int_\R e^{itx}f(x)\,dx$ for real $t$. Then $\widehat{u^*}(t)=\hat u(-t)^*$ for real $t$, and the equation
$$u*u^*=A \tag{1}\label{1}$$
for $u$ becomes the equation
$$\hat u(t) \hat u(-t)^*=\hat A(t) \tag{2}\label{2}$$
for $\hat u$.
Clearly, equation \eqref{2} can have multiple solutions. So, equation \eqref{1} can have multiple solutions.
E.g., suppose that $\hat A(t)=t^2e^{-t^2}$,
$$\hat u_1(t)=|t|e^{-t^2/2},\quad\text{and}\quad
\hat u_2(t)=e^{-t^2/2}\,t\,(2\,1(t>0)-\tfrac12\,1(t<0))$$
for real $t$. Then $\hat u_1$ and $\hat u_2$ are two different solutions of \eqref{2}.
The corresponding $A$ and solutions $u_1,u_2$ of \eqref{1} are given by
$$A(x)=\frac1{2\pi}\,\int_\R e^{-itx} \hat A(t)\,dt=
\frac{2-x^2}{8 \sqrt{\pi }}\,e^{-x^2/4}, $$
$$u_1(x)=\frac1{2\pi}\,\int_\R e^{-itx} \hat u_1(t)\,dt
=\frac{1}{\pi }
-\frac 1{\sqrt{2 \pi }}
e^{-x^2/2} x\, \text{erfi}\left(\frac{x}{\sqrt{2}}\right),$$
$$u_2(x)=\frac1{2\pi}\,\int_\R e^{-itx} \hat u_2(t)\,dt
=\frac{5}{4 \pi }-\frac x{4 \sqrt{2 \pi }}e^{-x^2/2} \left(3 i+5\,
\text{erfi}\left(\frac{x}{\sqrt{2}}\right)\right) \\
=\frac54\,u_1(x)-\frac{3ix}{4\sqrt{2\pi}}\,e^{-x^2/2} $$
for real $x$, where $\text{erfi}(x):=\sqrt{\frac2\pi}\int_0^{x\sqrt2}e^{z^2/2}\,dz$.
Here are the graphs of $u_1$ (blue) and $\Re u_2$ (gold) over the interval $[-6,6]$: