Can EndNote trawl references from hundreds of PDF ebooks, theses, journals & papers ?

I have accumulated hundreds of pdf, epub, mobi, djvu and chm files which contain thousands of references.

The literature covers fairly narrow medical topics.

Is it possible for EndNote (or any other application) to ‘batch’ search through such a collection and extract references ?

EndNote can’t search and extract reference lists within pdfs. You’ll need to find software that may perform this type of search and extraction function.

For example, Scopus (which is priopritory) can retrieve and export citations to Endnote.  Not sure what else -probably TR’s Web of Science (which I don’t use, sorry).    Seems that it is easier to export who cites something than who it cites in pubmed and on publisher web sites.    (but it isnt’ a trawl either, it would have to pull them each up)