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Well, probably your PhD is finished, but I have found a way to Insert Bibliography using Masters Document and Mendeley plugin.

  1. Go to View > Toolbars > Customize... there, in the Toolbars tab, click the Add... button.
  2. Under Category choose LibreOffice Macros > My Macros > Mendeley > mendeleyMain. Choose >_insertBibliography from the Commands list and click Add.
  3. Insert citations in each separate file as you usually do with Mendeley toolbar ("Insert Citation").
  4. In the Master Document, insert Text using the Navigator and, in this Text, Insert Bibliography using the Mendeley's button, now on your toolbar.
  5. Update All in the Master Document
  6. Now, go to File > Export... and choose the format ODF File Document (.odt)
  7. Finally, in this new .odt file, click on Mendeley's Refresh button.

Hope it works for you.