Yes, there shouldn't be two nodes for a single physical stop. But one of them is apparently regional, so the tags need adjusting (you left the service=regional ones). I am not sure which name is correct - there were two - it might need to go to alt_name. The route relations should remain on the node that is left - they might need to be transferred to a new node and member order kept. Transit area relation should include the node.

I didn't have the time to fix this, but it's not just "delete nodes". This has a bunch of things to consider.