Hi,
something went wrong here. You deleted the wrong version of the objects - removing the original one and keeping new ones with wrong tags like 

id = 289462654
relations = []
type= way


Your duplication issue happened 
because you loaded a geojson or similar file into JOSM and then try to upload it. You have to load data directly from the API or Overpass - every other way will lead to duplicates and not to editing the already existing objects.
