Since you've done everything by the book, you're probably in quite a good position. The two year break will not affect your overall entitlement to have FTB mortgage interest relief treatment for seven years - the only complication is that any calendar year in which you claim, or are entitled to claim, the tax relief (even if it's only for a month) is treated as a full year. So if you're in a position to move back to the apartment shortly as an owner occupier, you might be better to defer it until January to get the full value of the remaining years.