I have a ton of issues Importing and Exporting Localisation files, and have burnt too many evenings !
I usually resort to the XCode command line , that seems pretty reliable ....
I do a clean build maybe -SkipMacroValidation helps I cant recall !
/usr/bin/xcodebuild -sdk iphoneos -skipMacroValidation -configuration Debug -workspace my.xcworkspace -scheme myScheme build CODE_SIGNING_ALLOWED=NO
Then an Import or export
/usr/bin/xcodebuild -sdk iphoneos -configuration Release -workspace my.xcworkspace -scheme myScheme -importLocalizations -localizationPath path-to/my.xcloc CODE_SIGNING_ALLOWED=NO