I have here a site that uses the po plugin, and recently had this change committed to its setup:

 - de|Deutsch
 - fr|Français
-- ja|日本語
-- tr|Türkçe

The change was made by the web UI, so it must have involved a site rebuild at the time, as that configuration item has rebuild => 1.

Some days after that config change, a push caused ikiwiki refresh to fail:

remote: /home/b-udm/public_html/Discussion/index.ja.html independently created, not overwriting with version from Discussion.ja

Rebuilding the wiki cleared that up, but it seems that po plugin config changes can lead to follow-on problems of this sort.

The site still has a source/index.ja.po. And it has public_html/index.ja.html, as well as public_html/index.ja/index.html.