Xcode 3.2 : extension of the localized file subtree in the left pane (files and groups). Then remove the unnecessary localization. You might want to click the "Also move to cart" button.
Xcode 4 : select the file, show utilities box (on the right), select the "show file inspector" button. There is a section with localizations. Select unwanted, press the minus (-) button. Confirm. Or do it the way you did in Xcode 3.2 by removing the localization from the project navigator. It is up to you.
Xcode 5 : works like Xcode 4.
If you delete all localizations (for example, by mistake), you can add lproj folders to the project. You do not need to do one after another localized again.
Tip. Better do your work, experiment if your changes will not work on the previous version and try again.
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