>> running org-export-as-html on a subtree is currently problematic if >> the result is to be merged into a document which contains html-ized >> versions of other subtrees: the footnote references and definitions >> get clobbered.
Do the subtrees come from the same org file? Won't it look odd and confusing to a reader, when there are two different footnote definitions with the same number. Confusion is like to be pronounced, if the reader chooses to also print out the document as a pdf or into paper. --