This is still happening and confusing (at least to me, a new mod).
I think the merge function should be streamlined. Currently, there seem to be the following steps (at least for migrated duplicates):
- Close the duplicate
- Merge it into the main question
- Perform some action that cleans up the stub
Note that due to the current behavior, you must not delete the stub, as this would reject the migration.
It seems as if 1. and 3. could be done automatically by 2.
