Guys,
I had the same query a few months ago regarding annual totals and 'factoring'.
Having spoken to our fleet management the answer was that the factoring only applied during the life of the FCI that was issued, and after it expired our flying hours were to be counted one for one, and that the scheduling managers were aware of this.
The FCI concerned and the resultant factoring only applied from 21/8/2004 - 21/2/2005. I believe that scheduling are still using the factoring for their FTL calculations.