Doing it manually in Emacs was actually much less painful than expected.
It went something like this: open the .bib file, and for each entry
- select and copy (
M-w) paper title and/or authors to kill ring - do a fuzzy search with
gscholar-bibtex, - when there is a new version, insert it in place (i)
- (optionally search on biblio.el using the CrossRef backend and insert when relevant),
- reuse the BibTeX key.
The whole thing took about 30 minutes for 50 papers.