In this case, you can leave the student attached to both classes, and then when the new invoice is generated, you would need to manually edit the number of lessons this customer has to pay for.
Once you finished editing and approving the invoice - you can detach the student from the class he/she is not taking anymore.

For example:

Lolita was taking a Hip-Hop class, but decided not to move forward in the next season:

But she is going to take only one class.

So, we will generate an invoice for all classes she is currently attending (make sure its 'Draft':

And then under 'Actions' click on 'Edit':

And update the number of lessons for that class, the registration fee (if needed), and then 'Save':

Brilliant! Now you can approve and send it to your customer:

The final step - detach the student from the class list after the last lesson.