Just an update - as far as I can gather, having rang the TRS offices - you are only entitled to TRS for the first 7 years of your mortgage life, irrespective of any changes in circumstances.
So even if you get your FTB status back for stamp duty it does not apply to TRS.
Having said that the guy I spoke to in the TRS office did not fill me with confidence that he knew what he was on about - but I guess I'll just have to presume that he know he job!!