Hello! Thanks for the feedback and apologies for the very late reply - this post went completely unnoticed by us staff members.
This is probably a good conclusion. I assume that the information about the airport had been updated by the authorities, but that no new charts had yet been issued. This would absolutely cause trouble, and it should be super rare - well spotted! This likely affected real-world pilots as well 
As of typing this, however, the issue seems to be resolved. The new runway shows up on the chart, and the procedure charts seem to be correctly linked.
Thank you for posting this and again - sorry for the late reply!
Kind Regards,
Malte