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This link explains that the headless PDF conversion uses the last options set in the GUI PDF conversion, so the solution is to set the PDF/A option in the GUI then use the headless mode.

This link explains that the headless PDF conversion uses the last options set in the GUI PDF conversion, so the solution is to set the PDF/A option in the GUI then use the headless mode.

Or you can change the configuration file. The only thing that seems to be changed when the PDF/A option is toggled on is a number in the .libreoffice/3/user/registrymodifications.xcu file. The entry <item oor:path="/org.openoffice.Office.Common/Filter/PDF/Export"><prop oor:name="SelectPdfVersion" oor:op="fuse"><value>0</value></prop></item> has the value changed from 0 to 1.

The xcu file seems to be mostly one long line, so it isn't clear to me how best to edit it.