Yeah, helm bibtex is awesome. This has been a major topic of discussion in the 
module development. See: https://github.com/tmalsburg/helm-bibtex/issues/40

Last I talked with the developer, he was thinking hard about it and had maybe 
even started development on single-note file options. 

"Julian Burgos" <jul...@hafro.is> writes:

> Dear list,
>
> I have been using org-ref for a while, using reftex to insert citations in
> my org documents.  Now I am switching to helm-bibtex, which is pretty
> awesome.  I have a couple of question about the note files.  Org-ref uses
> a single file to keep notes (e.g. notes.org), but helm-bibtex assumes that
> notes are kept in separate files, one per article.  My questions are:
>
> a) Do you have a preference in the single file vs multiple files question?
>  Are advantages/disadvantages?  I tend to prefer the single file option,
> it makes search easy and also I can add TODO items that later I can pull
> out in the agenda view.  With multiple files this would not be as easy. 
> Do you agree?
>
> b) Helm-bibtex identifies which references have a note file, adding a
> symbol on the reference list.  Can we make helm-bibtex look into a single
> file (say the "notes.org" file), look for the :Custom_ID: properties of
> the entries, and use that to mark the reference list?  I am teaching
> myself emacs-lisp but this is above my capacity right now.
>
> Many thanks,
>
> Julian

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