OK so I think I found it, apparently I need:
[Internationalization]
+LocalizationPaths=%GAMEDIR%Content/Localization/MyLocalizationTargetName
In a game.ini. When I didn’t have that it defaulted the localization target name to ‘Game’ - which is set in the engine/config/basegame.ini but that’s not what mine was called.
Not sure how it worked before but adding that config entry fixed it after recompiling the text. Trouble is I’ve messed up all my translations in trying to work this out.