I think that when ja_wrong_auto_encoding.lyx was moved the inversion
regex did not match correctly.
# Japanese manuals use language "japanese" wich is tied to "platex"
# (automatically set instead of (plain) LaTeX).
# For export with other engines, the language must be set to "Japanese (CJK).
-# see also INVERTED.*export/export/ja/wrong_auto_encoding_(dvi|pdf(|3))
+# see also INVERTED.TODO_export/export/latex/ja_wrong_auto_encoding_(dvi|pdf(|3)).*
# For a discussion of alternatives for Japanese with LaTeX , see also
# http://www.preining.info/blog/2014/12/writing-japanese-in-latex-part-1-introduction/
export/.*/ja/.*_(pdf[245]|dvi3).*
export/doc/(de/|fr/)Customization_.*_systemF
# Error in Japanese document if LyX-logo is preceded by foreign language
-export/export/latex/ja_wrong_auto_encoding_(dvi|pdf(|3))
+export/export/latex/ja_wrong_auto_encoding_(dvi|pdf(|3)).*
# Missing characters with Latin Modern Unicode:
# 0000 NULL (where does this come from?)