\documentclass{article}

\usepackage{xstring}
\usepackage{hyperref}

\def\fmkeywords{Keyword1; Keyword2; Keyword3}

\StrSubstitute{\fmkeywords}{;}{,}[\fmkeywords]
\begingroup\edef\x{\endgroup
  \noexpand\hypersetup{
    unicode,
    pdftitle={My title},
    pdfencoding=auto,
    pdfkeywords={\fmkeywords}
  }}\x

\begin{document}

correct: \fmkeywords

correct: \StrSubstitute{\fmkeywords}{;}{,}

\end{document}