You are mixing up two separate issues here.
1) You need to get the mortgage into your own name. Let's assume, for the moment, that you lose your tracker.
You will have a mortgage of €97k @ 3% instead of 1%. So it's a difference of about €2,000 in the first year, and reducing after that as you repay the capital. Not good, but not the end of the world either.
2) Are you sure that you will lose the tracker? Have you asked BoI? If you can afford it on your own, they may allow you to keep the tracker.
3) If they refuse to allow you to keep the tracker, would your ex-wife allow her name to stay on the mortgage? Then BoI doesn't need to know. You just keep paying the mortgage.
4) Sort all that out first and then worry about the extension. If it's not urgent, then postpone it until you see how you are getting on with the higher mortgage repayments.
5) If your ex does agree to allow her name to stay on the mortgage, presumably she will object to having her name on an increase in the mortgage.