To find .bib files, reftex uses `reftex-locate-bibliography-files', which in turn checks whether bibtex is in use via `reftex-using-biblatex-p'. The latter is too naïve: it only checks if "biblatex" is amongst the `TeX-active-styles' or does a simple syntactic check of the current buffer. In case \usepackage{biblatex} is loaded in, say, an included file, these checks fail, and the use of biblatex is not detected. As a result, only the first of potentially several \addbibresource{fooN.bib} statements is picked up, and subsequent bib resources aren't parsed by reftex.
This is doubly unfortunate, because auctex's "style" (black) magic exposes `LaTeX-bibliography-list', which does pick up the different bib files, and could be used in reftex when available.