You can patch the subequations
environment with etoolbox
's \patchcmd
to use \Alph
instead of \alph
:
\documentclass{report}
\usepackage{amsmath}
\usepackage{etoolbox}
\patchcmd\subequations{\alph}{\Alph}{}{\GenericError{}{Patching failed.}{}{}}
\begin{document}
\begin{subequations}
\begin{align}
3 &= 1+2 \\
6 &= 2+4
\end{align}
\end{subequations}
\end{document}

EDIT: If hyperref
is already loaded, instead of patching subequations
we have to patch HyOrg@subequations
. The following does so (without testing whether hyperref
is actually loaded):
\documentclass{report}
\usepackage{amsmath}
\usepackage{etoolbox}
\usepackage[]{hyperref}
\makeatletter
\AtBeginDocument
{%
\patchcmd\HyOrg@subequations
{\alph}{\Alph}{}{\GenericError{}{Patching failed}{}{}}%
}
\makeatother
\begin{document}
\begin{subequations}
\begin{align}
3 &= 1+2 \\
6 &= 2+4
\end{align}
\end{subequations}
\end{document}
EDIT2: If you can control when hyperref
is loaded, you can simply do the patching of the first code in this answer, and load hyperref
afterwards. hyperref
uses the definition in effect when it was loaded.