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Well the issue for me is that the document is now hard to read, much like a .tex source file. Theorem environments are possible in LyX, but they are not recognised.

This is pdfTeX, Version 3.14159265-2.6-1.40.17 (MiKTeX 2.9 64-bit) (preloaded format=pdflatex 2016.9.9) 13 OCT 2016 14:05
entering extended mode
**./test.tex
(test.tex
LaTeX2e <2016/03/31> patch level 3
Babel <3.9r> and hyphenation patterns for 75 language(s) loaded.

("C:\Program Files\MiKTeX 2.9 ...

I guess my problem is slightly different. It will still compile, but the theorem environments are not recognised by LyX.

So as an example document:

\documentclass{article}
\usepackage{amsthm}

\newtheorem{thm}{Theorem}

\begin{document}
Test

\begin{thm}
Test theorem.
\end{thm}
\end{document}

I ...

Yes i did this. I loaded amsthm in the preamble. It still does not work for some reason.

I'm having the exact same problem in LyX version 2.2.1. Would really appreciate a solution.

Seems trivial to fix to me...