Hi @SteelWagstaff, I don’t think we can realistically support nested shortcodes in our footnote shortcode. The reason for this is that the footnote content is wrapped in an inline tag and then positioned using the CSS Generated Content for Paged Media for Prince (PDF) output (this lets them appear at the bottom of each page rather than as chapter endnotes). The necessity of using an inline tag means footnotes can’t contain block elements like paragraphs and lists, so we have to do a lot of hacky stuff to get more complex footnotes to display properly (see also this topic). I expect if we enabled shortcode nesting for our footnotes shortcode we would fully break PDF outputs. Also, given the advent of Gutenberg, we are going to need to revisit our footnote methodology anyway…
All to say that this is probably not an easy integration to support. I think the best approach would be to clarify your use case (how do you want an integration with Zotero to work?) and see if there’s a better solution we can develop. I know we have some work to do to add Zotero-compatible metadata but I have yet to get a clear specification on how to format metadata for Zotero (see here).