@MaxiPalle I just tested this and it is working for me on S9 Baro Here are the steps:
Make sure to force quit MC app
Open SA and do NOT unpair from SA, simply forget the watch from the app, then select ok.
Force quit SA.
Open MC, the watch will automatically sync (if you select a route on the computer first, the route will sync). If you did not select a route on the computer but you select from the app, you will need to force quit MC and restart the app to restart the sync. The route will now sync with waypoints. Check to make sure the sync is finished.
Do not unpair from MC app, force quit MC
Open SA and select the watch to pair from the watch menu, it will connect and sync.
You will lose custom sport modes from SA and have to set them up again but routes from MC with waypoints are retained.
This is working for my S9baro with no issues I am on iOS13.3 and the latest SA beta.