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Deleting the last entry of a mapping or sequence via config/set orphaned ruamel's comment tokens, which were then emitted above a flow-style {} / [] at column 0, which is unparseable yaml that failed validation and silently rolled the change back. The fix is to clear the emptied collection's stale comment metadata (and the parent's entry for it) so the dump stays valid. Non-empty collections are left untouched so sibling comments are preserved. This covers both emptied maps and emptied lists.