If there’s no adjacent text that the linked comment can be attached to, Scrivener inserts the “linked comment” text to provide an anchor, so that the annotation isn’t lost during conversion.
My fault, I didn’t understand earlier what you were describing. There are legitimate cases where the “Linked Comment” text is added to prevent the annotation just floating off, and I thought you were just asking about how that came about. I see the bug you’re talking about with the repeat conversions–it’s like Scrivener is still seeing the previous text as linked, so it’s adding the new “Linked Comment” text to avoid overwriting a non-existent comment. If you close the project and reopen before you run the conversion again, it seems to work correctly.