OP, you had reminded me to reinstate my own TRS. What you need to have done is (i) cancel TRS on any of the old mortgages, (ii) apply for TRS on your existing loan (you can do it online [broken link removed]) and (iii) (this is the bit I had to do today) recommence TRS, which you can do online [broken link removed].
It sounds like you've done (i) and (ii) so I think all you have to do is the recommencement form in order to sort yourself out. They said to me to give them a shout by April if the refund hadn't been sorted out by then. They were v helpful indeed, although the wait to get through was quite long.