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When I do \input{file} in a .tex document I later import in LyX, LyX converts file.tex into file.lyx and changes \input{file} to \input{file.lyx}. But LyX doesn't do well with the TeX code it does not support natively and \input{file.lyx} is a rather corrupted conversion.

How can I make LyX just pass the code from file.tex to pdflatex as a part of a bigger file without LyX making any conversions?

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"Hide" \input from LyX by adding to your preamble (Document > Settings... > LaTeX Preamble)

\let\fileinput\input

and then use

\fileinput{file}

in your document.

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