The warnings were noted before about a year ago: https://lists.launchpad.net/kicad-developers/msg12412.html
That includes fix for at least one bug: There are still some warnings in the the pcbnew/pcbd2kicadpcb_plugin. I haven't touched it because the module lacks of documentation and I don't want to screw it up. The patches fix at least one minor bug: Find in eesheme haven't searched through error markers.
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