I have gone back to check and agree that relief may be due.
The replacement condition at 3(6)(d):
at no time during the period beginning with the effective date of the previous transaction and ending with the effective date of the transaction concerned has the purchaser or the purchaser's spouse or civil partner acquired a major interest in any other dwelling with the intention of it being the purchaser's only or main residence.
It all depends on whether the flat can be regarded as a residence. If it is not a residence then the next purchase will be a replacement for the old one (provided it is within 3 years: but the longer it takes the more likely the flat will be a residence). If it is a replacement, the extra 3% does not apply.
It's also worth noting that if the flat is a residence you will get CGT reliefs when you sell it. If it is not a residence, you won't.