It's not the best practice to shut it down during a regeneration but shouldn't hurt it. My feelings about the whole thing is I just try and limit it's cycles by watching my CS2 and let the truck complete it's process. I figure the components have a certain lifespan, and if I can eliminate partial burns then I'm ahead of the game.
As far as you going on a long drive after work, unless you have a monitor to force a regeneration, you won't get into another until you reach the 66%+/- threshold...
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I live in southern Or and vehicles have to pass DEQ- visual and emission testing, so removing emission stuff isn't an option until vehicle is 21 yrs old.