The issue here is was the disposal recorded in the correct period and was the CGT paid in the appropriate period (a) or (b) in the relevant year. If it was, then I can not see Revenue having any case and I would be asking them to state the basis for the charge.
However you mention disposals in 2007 being returned in 2008 returns and the CGT being paid in November 2008.
The rules for 2007 were that CGT on disposals in the period 01/01/07 to 30/09/07 were to be paid by 31/10/07 and CGT on disposals in the period 01/10/07 to 31/12/07 was to be paid by 31/01/08. Was the CGT payment made late therefore? ( reference here S.950-959 TCA 1997)
Also, you mention disposals in 2007 being returned on the 2008 tax return. Surely the 2007 disposal should have been returned on the 2007 tax return and filed by 31/10/08?
You mention interest of over €100K in that case, obviously the CGT paid was a substantial sum. I imagine they are looking at material CGT payments to see if they were paid on time and if not then to see if there is anything further to be collected.
Separately, but related, I've had a number of recent Revenue enquiries asking for listings of investment properties to be given, when purchased, disposed, rents etc. for clients. It appears they are taking more interest in those areas.