From Jürgen:
LuaTeX support in polyglossia is still very new and experimental.
I have this enhancement on the agenda for 2.2, but not for 2.1.
For more details, see:
http://marc.info/?l=lyx-devel&m=
138506346715339&w=2
export/examples/he/splash_pdf5
export/examples/he/splash_dvi3
#
+# Greek docs do not currently work with LuaTeX
+# This should be fixed for LyX 2.2
+# See http://marc.info/?l=lyx-devel&m=138506346715339&w=2
+export/doc/el/Intro_dvi3
+export/doc/el/Intro_pdf5
+export/examples/el/splash_dvi3
+export/examples/el/splash_pdf5
+#
export/doc/hu/Intro_pdf5
export/doc/id/Intro_pdf5
export/doc/id/Shortcuts_pdf5