+1 Identify issue.
1. Identify issue
2. Could be as simple as seating a bit deeper, adding a bit more crimp, or using an FCD as normal.
3. Could take using an FCD with a push through adaptor.
4. Instead of the above, you might find it easier to do a chamber check on all your rounds, and set aside those 1 in 20 that don't chamber. The FCD push-thru technique takes a lot of force and 6k pulls is going to suck.
5. If all else fails, I think I'd rather go out and buy a new gun that'll chamber those rounds, rather than pull them all.
6. If you're really up to pulling 6k bullets, I'd investigate the possibility of buying or making a collet type bullet puller. I'm thinking of taking a cheap pair of pliers, grinding out a bullet shape in the jaws, and padding it with rubber to make a custom bullet puller jig that you use with your press on the downstroke. 40SW is probably the worst cartridge to pull bullets this way, though. Darn long case and short bullet protrusion is going to make it a bugger. And that would be the easy part. You'd also need some kind of extension to get the shellholder high enough so the bullet would poke out the top of the ram!
Considering RMR is selling pulled pistol bullets by the truckload, you might wanna ask around. There's got to be an easier way to pull 6k bullets.