Brian Litz has an excellent chapter on this topic in one of his books - well worth reading.
He basically says change the variable that you have the least faith in.
There is a fair amount of documented research for most of the modern projectiles, and you should be able to get a validated BC (G7) for them.
DO NOT trust what the manufacturer tells you their BC value is, it is marketing. Let me know which projectile you are using and I can look it up in Litz's book.
Chronographs, unless you are using a LabRadar, are not exactly precise instruments, so muzzle velocity would more than likely be the variable I change first.
The other thing to confirm is that your turrets are calibrated correctly. Shoot a "tall target" and get a good 100yd zero, then dial up 10 or 20 minutes, and measure the shot fall.
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