It's not only removing the wikilink that causes the issue, but any change to the same table cell (like adding text or changing link label).

Minimal test case is just [[a|b<ref>c</ref>]]: https://en.wikipedia.beta.wmflabs.org/wiki/T352624 – just about any edit to that page causes the <ref> to be lost.

(on that page, I also see an exposed strip marker in the old parser, which isn't the case in the original Wikipedia example – interesting)

Maybe related: T303409: Linter for "references in links", T289491: Corruption in edit involving <ref> in external link

$  echo "[[a|b<ref>c</ref>]]" | php bin/parse.php --wt2wt
[[a|b]]<ref>c</ref>

<references />

But yes, this is just a fallout of trying to embed A-tags (introduced by the reference) inside A-tags (introduced by the wikilink). Parsoid has some code in place to detect link-in-link scenarios but that analysis runs before ref-tags are processed. So, unless this and T289491 are *not* edge cases, my preference is to just have T303409 flag them as broken wikitext that should be fixed up instead of trying to add complexity inside Parsoid to detect and recover from them.