None off the existing solutions (from chapterbib to biblatex/biber) cares about how you organize the bib-entries in the bib-files. You can use one or ten bib-files. With biblatex you can use refsections or refsegments to split the bibliographies. Here an example for refsegment. I used \section instead of \chapter to get everything on one page, but it works for \chapter too.
\documentclass{article}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage[refsegment=section,style=authoryear]{biblatex}
\addbibresource{biblatex-examples.bib}
\begin{document}
\section{first}
\cite{doody}
\printbibliography[segment=\therefsegment,title=first bib]
\section{second}
\cite{herrmann, doody}
\printbibliography[segment=\therefsegment,title=second bib]
\end{document}
