Generally speaking, whenever one submits an manuscript for publication there comes a time when the inserted bibtex bibliography must be replaced by the corresponding bbl file. I know a way to do this: to find the temporary bbl file generated with when you view the LyX file. But the process takes several steps. Given that we face this every time we publish an article or book, would it make sense to make the inclusion of the bbl file a menu choice? Something like Export > LaTeX (pdflatex with bbl), say?
Bruce Pourciau