I have two matrices, $A$ and $B$. I was (perhaps naively) expecting them to be more-or-less similar ("more-or-less" because this is in a numerical setting), but instead of having exactly the same eigenvalues, two of the eigenvalues are the negation of the corresponding ones in the other matrix.
$\operatorname{eig}(A) = \{ \cos(\theta) + i*\sin(\theta), \cos(\theta) - i*\sin(\theta), 1, 1\} $
$\operatorname{eig}(B) = \{ -\cos(\theta) - i*\sin(\theta), -cos(\theta) + i*\sin(\theta), 1, 1\} $
What does this imply, besides that they are not similar? Can they be made similar, by negating the two "problematic" eigenvalues and the corresponding eigenvectors, or something?
If the matrices $A,B\in M_n$ are nxn, then yes.
Since those eigenvectors have the same complex modulus, you can rotate matrix B to be in the same plane as A. That rotation matrix is nonsingular, therefore you can combine it with the matrix that diagonalizes $A$ to get a nonsigular matrix that makes it similar to $B$.
For instance, for $A,B$
$$\operatorname{eig}(A) = \{ \cos(\theta) + i*\sin(\theta), \cos(\theta) - i*\sin(\theta), 1, 1\}$$ and $$ \operatorname{eig}(B) = \{ -\cos(\theta) - i*\sin(\theta), -cos(\theta) + i*\sin(\theta), 1, 1\}$$
Both of the matrices have n distinct eigenvalues, so find nonsingular matrices that diagonalize them.
$$ S^{-1}AS = diag(-\cos(\theta) - i*\sin(\theta), -cos(\theta) + i*\sin(\theta), 1, 1)$$
Then just multiply this matrix by $$ I = \begin{vmatrix} -1 & 0 & 0 & 0 \\ 0 & -1 & 0 & 0 \\ 0 & 0 & 1 & 0 \\ 0 & 0 & 0 & 1 \end{vmatrix} $$
Since similarity is transitive, you have that $A$ is similar to $B$.