You can do what you like with the money. All the Tax Credits people need to know is if you have got more than �300 in a year in interest or dividends from your savings - not the amount of the savings thermselves.. If you pay off your mortgage you will no longer have the money so this will not occur.
The rules are quite different for means tested DWP benefits such as Council Tax Benefit or Income Support. With these, you have to declare any savings and there is an upper limit of �16000.