whilst a cheque is deemed to be "stale" after 6 months, it is banking practise and not enshrined anywhere in law. Therefore your bank is within their rights to debit you if the cheque is lodged but also to bounce the cheque( and possibly charge you a fee for that).
You've actually paid the debt, it's not your fault if they have not got around to lodging it, that's their problem. However in case they lost the cheque, I'd suggest that you contact them to see what the story is, and if they think they haven't received it and that you still owe them money, place a stop on the original and issue them with a new cheque. Whatever you do, do not issue a 2nd cheque without placing a stop on the original