During flight testing, the aircraft's engine(s) power is calculated. However, this power is usually not used for FM calculations, instead a lower power level is assumed (for example a "minimum" engine), corresponding to the least powerful NEW engine that may be accepted be the aircraft manufacturer. The ratio between these levels is something of an educated guess, but usually one ends up with the right numbers (no guarantee, however). This adds some safety margin as well.
Engine degradation due to flight hours is usually not taken into account,
AFAIK. But manufacturers may be able to provide you with the numbers to expect.