If you use the tool, close it, and return later to finish the article, references will be empty and the reused ones will be wrongly numbered (since there's no content and they're all considered unique references).
I used this tool to translate a few articles, and I've always had this issue. The only way to work around this is to either finish the translation in one go, or translate the text first, then insert all of the references later, right before publishing (which makes it difficult to keep track of variations and supplementing one might be doing for their localized Wikipedia page).