You will not be charged for the meter.
Your usage will be worked out in your favour but if you disagree say something to them.
You will not have to pay it back at once although you will have 12 dd payments on your account(assuming you are on a monthly dd) and they should cover it.
I think it would be difficult to say that SE are response for checking your meter is running properly your meter gets read ever 6months and it may be a diff reader.
You should have had 4 bills in that time and SE and you should have noticed that there had been no usage. Nobody uses no gas in december for example! lol!
Bills will be produced automatically and they would more than likely rely on you noticing that you had used no gas for the past however many months.