There might be some incorrect or unexpected behavior when switching output engines in LyX, because Xetex does not support input-encoding settings:
To reproduce: Start a document, go to setup: - first try something for pdflatex and define under language: input encodig to other (here it was utf8) (then close dialog, reopen dialog and) - switch to fonts, set these to any combination of luatex/Xetex. Try to compile the document. It will complain that inputenc is not suitable for the chosen engine. But then going back to doc-settings and just trying to unset the other(utf8)-option back to default is inaccessible (greyed out). To do anything about that you have to first also unset your font-settings back to choices for pdflatex. This is wrong imho. I think LyX should keep these settings for the usage case "switching engines" but gracefully ignore inputenc settings for Xetex. This was presumably intended to keep users from messing with inputenc once Xetex was the chosen output engine for a document, but it is confusing when you only find out later that you might have to use Xetex instead of pdflatex. gretings Mike