I want to specify encoding that is used by Lyx when it generates LaTeX source for preview or export. That is not a big problem Document->Settings->Language->Encoding->Other->Select encoding from combo box will do just that. But it will also add command \usepackage[selectedEncoding]{inputenc} to preamble of generated document.
How do I prevent that? I want all my LaTeX documents to be generated in UTF-8 but I do not want that inputenc declaration in preamble.

inputencdeclaration is it a problem? – Paul Gaborit Dec 26 '12 at 02:01inputenctherefore there is option clash possible. See http://tex.stackexchange.com/questions/88177/option-clash-for-package-inputenc-when-using-lyx-with-latex-class-that-already-u – Rasto Dec 26 '12 at 14:42