An empirical solution could be to use the Grover's Diffusion Operator $D$.
Lets say the qubits are in an initial state $|\psi\rangle = \sum_{0}^{2^n-1}\alpha_i|i\rangle$. Since global phase/sign is irrelevant. We can assume that phase/sign of $\alpha_0$ is + for the sake of convenience (If $\alpha_0=0$ choose the lowest index with non-zero amplitude).
We can find the constants $|\alpha_i|\forall i$ by taking square roots of probabilities and hence we can assume their knowledge.
Grover's Diffusion Operator maps $|\psi\rangle = \sum_{0}^{2^n-1}\alpha_i|i\rangle$ to $D|\psi\rangle = \sum_{0}^{2^n-1}(2\mu-\alpha_i)|i\rangle$ where $\mu = \sum_{0}^{2^n-1}\alpha_i$. We can find the probability distribution of this state and let us say we now also have knowledge of $|2\mu-\alpha_i| \forall i$
Using values of $|\alpha_i|$ and $|2\mu-\alpha_i|$ we get 4 possible values of
$\mu = \frac{\pm|\alpha_i| \pm|2\mu-\alpha_i|}{2}$.
Remember we have $2^n$ values of $i$ each which can give us a group of $4$ possible values of $\mu$. We find the common value of $\mu$ across all these $2^n$ groups of $4$.
Since we assumed $\alpha_0>0$ we only get 2 possible values of $\mu = \frac{|\alpha_i| \pm|2\mu-\alpha_i|}{2}$ So at max there can only be $2$ values of $\mu$.
Hopefully we have narrowed down to a single value of $\mu\ne0$. If we have then we can use it to easily calculated $\alpha_i$ from $|\alpha_i|$ and $|2\mu-\alpha_i|$ thus giving us the sign information for all $i$.
If $\mu=0$ or there are $2$ possible $\mu$ then we must modify the original state. A possible solution is too selectively flip the sign (using $Controlled$ $Z$ gates) if and only if the state is $|j\rangle$ for some $j$ which has an amplitude $\alpha_j\ne0$.
This will result in a new $\mu'$ which cannot be zero if $\mu=0$. Applying same procedure on this state will yield 1/2 value(s) which can be used to deduce original $\mu$. Since $Z$ gate only changes sign but not magnitude of amplitude the probability distributions will remain same.
I know this isn't a complete formal solution but hopefully it helps.