I have had the same problem with the Germany extract from Geofabrik (the
Bodensee and part of the Rhine was empty). Caused by incomplete multipolygons
at the border regions due to the cutting. I download those complete relations
with overpass and add them to the germany-latest.osm.pbf with osmconvert:
%DIR%\tools\wget.exe
"http://overpass-api.de/api/interpreter?data=(relation(1685222);node(r)->.nodes;way(r);node(w););out
meta;" -O "%DIR%\resources\rhein.osm"
%DIR%\tools\wget.exe
"http://overpass-api.de/api/interpreter?data=(relation(1156846);node(r)->.nodes;way(r);node(w););out
meta;" -O "%DIR%\resources\bodensee.osm"
%DIR%\tools\osmconvert.exe --drop-version
%DIR%\%date%\Splitter\germany-latest.osm.pbf %DIR%\resources\rhein.osm
%DIR%\resources\bodensee.osm --complex-ways -o=%DIR%\%date%\Splitter\DE.o5m
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