I've been cleaning up old stuff on my account and I recently used the Move to Vault tool to empty all of my old legacy shops. On that page it says "Once the transfers are done, your now-empty legacy shop will be deleted." My legacy shops are still showing on the "Commerce">"Your Shops" site navigation drop down. They are all gone from the drop down on the Move to Vault tool page.

Just wondering since it's been about a day since you posted this, did they ever go away on their own from the navigation drop down? If they did, it may have just been a case where the cache needed some time to catch up.

I had the same thought but they are still there as of right now, so I doubt it's just the cache.