To extract the subset of the consolidated bib file that a particular paper uses, it is possible to use JabRef.
Here it is also worth to point out that a situation when a cited reference is missing from the bibliography can be detected using the following (assume "make" calls the latex command, namely: latex doc; bibtex doc; latex doc; latex doc):
make | grep -i "warning--" | less
This at best is a hack, but I could not find a better way till now. In particular, there seems to be no easy way to make missing bibentry as an error.