In Content Translation it is possible to work in translations in several sessions. A user [[ https://www.mediawiki.org/wiki/Topic:W5cazyhyu0alokyk | reported ]] that continuing an in-progress translation results in problems with the references: "references will be empty and the reused ones will be wrongly numbered (since there's no content and they're all considered unique references)"
Restoring a saved translation should recover the contents without any loss. We may need to investigate which may be the cause for this not to happen with references.
Another user in T293868 reported the issue may be more general, affecting other kinds of templates. This was illustrated in [[ https://people.wikimedia.org/~urbanecm/screencasts/T293868.webm | the following screencast ]].
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May be related: {T261170}