CGT and PPR

Briefly,

Client purchased a property in 1990 which was mainly let until disposed of in 2009 (let for appox 15 years total).

No PPR election was made within the 1st 2 years of purchase of the property.

Client was not resident in the property until July 2008, at which time the client was resident in the second property for a period of 3 weeks while attending daily hospital appointments. The second property is approx. 2 hours drive from the main residence but 5 mins from the hospital. Revenue was informed of a change in PPR in relation to this period of residence.

In April 2009, client disposed of the second property claiming PPR for the final 36 months of ownership and letting relief to the extent of the PPR exemption, saving a modest amount of tax.

Unsurprisingly the revenue have opened a compliance check. My question is - is the PPR claim valid on the second property. My client was definitely resident for this period, but as he was outside of the 2 year window for making an election can he claim PPR?