I think this affects Wikidata as well – I just added separate and distinct yue and zh-yue labels to the sandbox item, which probably shouldn’t be possible. It looks like both MediaWiki (meta=languageinfo) and Wikibase (meta=wbcontentlanguages) consider yue and zh-yue to be different languages to some degree (albeit with the same name and autonym).

The same seems to be true for other deprecated language codes, e. g. als (⇒ gsw) or be-x-old (⇒ be-tarask).

Likely related to (possibly a duplicate of) T44396: duplicate/invalid language codes.

That task notes that the regular Wikidata user interface already doesn’t allow you to set terms using deprecated language codes – if you add e. g. ?uselang=zh-yue to the URL, MediaWiki normalizes it (in this case to yue) before Wikibase ever sees it. (The example edits I linked above were made via Special:SetLabel, which doesn’t use the user interface language and so still allows those language codes.) Maybe the Commons app should apply a similar mapping even if the underlying Wikibase problem isn’t fixed soon (so it would still be possible to set zh-yue via the API, but it wouldn’t happen so often through the Commons app).

I believe this is working on 2.7.50315-alpha-2020-04-16

@TheDJ nothing has ever changed and the problem remains the same since this task was opened in 2020. still possible to add zh-yue captions. old captions still not migrated. there was no reason that this was closed when nothing was changed at all.