Custom hierarchal taxonomy loses interface hierarchy when selecting parent & children

This seems to be normal, it also happens for categories. The wp_terms_checklist(), which creates the checklist, has an argument checked_ontop, enabled by default. The metabox does not override this, so checked categories or custom terms always appear on top of the list. This does not affect their actual hierarchy, only how they are displayed there. It seems the remaining items of the hierarchy, that “lost” their parent, are added to the bottom.

I do not think there is a sensible way to override this, unless you want to duplicate the whole meta box code.

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