I have dt register with some events and der registration email to the customer was modified. The emailed result was after the modification still the old version!
I looked up inside the event, but the special email is not active there.
Once the email is changed, the original is lost so there is no way the old email will still be sent. What must be happening is you are modifying a different email than what is actually being used. There is the thanks email in the main configuration area which will be sent UNLESS you create/enable a custom thanks email in the event.