\screen_font_encoding is an xforms-only setting that is ignored by lyx-qt on purpose. The encoding of fonts is transparently handled by qt, and LyX has no chance to influence it. If you have encoding problems with LyX then the reason is not a wrong font encoding, but something on a higher level: LyX may internally need a different locale than you are using, because up to version 1.4.x it does not understand unicode. See http://bugzilla.lyx.org/show_bug.cgi?id=1755.
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