Joining elements that belong to a group (regardless you are inside of "group editing" or not) only elements in that instance are joined, so you have to repeat the operation as many times as instances of that group you have.
This is something that goes against the meaning of making groups.
My suggestion is:
- If you use the join tool within the group editing, the elements will be joined in all instances of the group.
- Conversely, if you use the join tool outside of the group editing, it will only affect the elements in that instance.
