It sounds complicated. What I read in their paper is the following:
"We iteratively construct BBH initial data, tuning the initial data to achieve a BBH
with the desired properties. Our iterative scheme uses two nested loops. The inner loop
solves the XCTS equations, adjusting our choices for the free data (conformal metric,
trace of extrinsic curvature, and the time derivatives of each) and boundary conditions,
until the resulting BBHs have the desired mass ratio and spins [132, 133]. The outer
loop briefly (typically for a few orbits) evolves the initial data resulting from the inner
loop, and adjusts the initial coordinate velocities to yield a BBH with small orbital
eccentricity [46,47,134], typically e0 ∼ 10−4 as defined in Eq. (17). For some simulations
in the SXS catalog, we intentionally omit the eccentricity-reduction loop, to obtain initial
data for BBHs with non-negligible orbital eccentricity."
They also say, "Here Ncyc is approximated by doubling the
number of orbits during inspiral up to merger (when a common horizon forms), as
determined by the coordinate trajectories of the black holes."
So it sounds to me like they are doing the following:
(1) They have some definition of the start of the inspiral, probably determined by the rate of change of the orbital period.
(2) They then count the number of cycles (call it N) from the start of inspiral until coalescence.
(3) They then double this to give Ncyc = 2N. So they start N cycles before the start of inspiral, as defined in step 1.
If this is the case, then the only question is how they determine the start of insprial in step 1. You could try looking at your extracted waveforms Ncyc/2 cycles from the beginning and see if you can determine what they are doing. Or in the "Help and Documentation" tab, there is a link to send them an Email, so you could ask them.