Stevenage Borough Council appear to be doing it right
Had a letter arrive yesterday explaining the changes and stating that I am "not listed on the open register" which matches the opt out I made a number of years back
The letter also has info about what the two registers are as well as a url for more info about the changes (www/gov/uk/yourvotematters) and the the last paragraph has instructions about how to change the opt in/out status by either email, phone or in writing