Version in BizTalk is very difficult. Basically, you need to treat the new version like a totally new schema – which it is. Side by side versioning is extremely hard.
You’ll need to make sure you change the versions on the maps, inside the Orchestrations (message variables and on the ports), and set your pipelines to use the correct schema version.
Inside BizTalk Admin, it might be sticky. If you have removed the older version and still see it. Not really sure there.
Best of luck.