Assume I can express a rank-deficient, $N\times N$ symmetric covariance matrix $\Sigma$ as
\begin{equation} \Sigma=\mathbf{USU}^\top \end{equation}
where $\mathbf{U}$ is an $L\times N$ orthonormal matrix, i.e. $\mathbf{U^\top U}=\mathbf{I}_L$.
I am wondering whether the Frobenius norm $|\Sigma|$ is equal to $|\mathbf{S}|$. I can see how this is true for the special case where $\mathbf{U}$ is an orthonormalizing (eigenvector) basis (so that $\mathbf{S}$ is diagonal), and haven't been able to show otherwise in numerical experiments, but I'm not sure how to evaluate more generally.
The answer is yes. Note that $$ \begin{align} |\Sigma|^2 &= |USU^T|^2 = \operatorname{tr}[(USU^T)(USU^T)^T] \\ & = \operatorname{tr}[US(U^TU)S^TU^T] \\ & = \operatorname{tr}[U(SS^TU^T)] = \operatorname{tr}[(SS^TU^T)U] \\ & = \operatorname{tr}[SS^T(U^TU)] = \operatorname{tr}[SS^T] = |S|^2. \end{align} $$