I have no idea what’s going on, but either Translate’s source code is quite broken, or the database has been corrupted.
When I try to mark [[https://meta.wikimedia.org/wiki/Template:Navigation_header/COVID-19|m:Template:Navigation header/COVID-19]] for translation, I have the option to turn on translation-aware transclusion (it’s off) and to upgrade to the latest syntax version. However, the syntax version has already been upgraded in October ([[https://meta.wikimedia.org/w/index.php?title=Template:Navigation_header/COVID-19/de-formal&diff=20509452|example edit by FuzzyBot adding the new markup]]), and the main COVID-19 page’s [[https://meta.wikimedia.org/w/index.php?title=COVID-19&oldid=21436040|May 8, 08:35 version]] (the one before @1234qwer1234qwer4’s today revert) wasn’t full of raw `<translate>` tags when [[https://web.archive.org/web/20210508141502/https://meta.wikimedia.org/wiki/COVID-19|archive.org saved it]] a few hours after that May 8 edit, meaning the translation-aware transclusion was turned on at that time.
The translation-aware transclusion could in theory been turned off since archive.org saved the page, but the syntax version update cannot be undone on-wiki, only directly in the DB, so something’s broken for sure.
== Outcome
Translatable page settings are no longer disappearing unexpectedly.
There was a bug, which got more severe recently, which caused a silent and permanent deletion of settings of translatable pages when associated translation page was deleted (see https://www.mediawiki.org/wiki/Help:Extension:Translate/Glossary). Such settings include priority languages, syntax version and transclusion support and other metadata.