I was following this guide on producing a layered PDF from QGIS, but somewhere along the way I seem to miss something. Exporting layers via the composer into a svg works fine, also loading the svg into scribus, splitting the groups and shifting the polygons to a new layer works.
Perhaps my question should be attached to Can QGIS preserve layers when exporting to PDF? from 2015.
Trying this under Win7, using QGis 2.18.11, Scribus 1.5.2 and Acrobat Reader XI.