As long as you're aware that exposed lead bullets will increase the need for cleaning, I'd shoot them and not worry about it too much. All that I shoot in my USC45 conversion is .45ACP Semi-wadcutter, Lead and it's a steady diet. On average, it sees about 99% lead bullets and the remaining 1% are FMJ ball through the suppressor.
The .40 round is about twice the chamber pressure of a .45ACP, so that additional velocity and pressure is going to cause a lot of lead to be stripped off and will build up in the polygonal bore. As long as you clean it every couple of hundred rounds - complete with bore scrubbing - you should be just fine.
I would stress that you should *NEVER* fire FMJ .40 through that barrel after you've fired a bunch of lead - this will lead to even higher pressures than the .40 FMJ develops on it's own and could lead to catastrophic failure if you have a lot of barrel leading and try to shove a hard FMJ round through all of it.
As to accuracy - you can expect to lose a little accuracy pushing a bullet that fast and with that much pressure without a hard interface to the polygonal rifling. That's just part of the equation when you shoot lead.
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