Yes, I think some CGT is inevitable, but there could be a real problem in calculating how much in a situation such as you describe. If there is a lot of money at stake it could be worthwhile getting advice from an accountant who is experienced in CGT matters - or your ex should do so as it is probably him who has the CGT liability as he is the sole owner.
Having said that, I'm not sure I understand the position. If he became the sole owner 16 years ago, under what legal provision are you entitled to a share of the equity now? I know that in divorce cases a deferred payment of equity of this kind can happen, but have always understood that the house stays in joint names until the payment is made. If what has occurred is that your interest is secured by a charge on the house (rather than you being a joint owner) then it seems that what you are owed is more in the nature of a debt. If that is the case, then I am not sure that CGT will apply because the debt is a civil matter and nothing to do with realising a capital asset. I may be barking up the wrong tree here, but I would certainly get professional advice on it.