Updating Carbonite should not change the settings for your characters in any way, as long as all you delete prior to the update is the Carbonite folders in your "AddOns" folder (which is all you should do, anyway). If you use "Minion" you don't even have to worry about it. It's all done for you. Carbonite's settings are kept at a separate location, so, no worries there.
As for the BG maps, I don't know. I don't do BG's, so have no idea what happens with the map and it's settings there. When you import the settings from another character, as far as I know, it imports them all.
Edit: After thinking about this, I scanned the "CarboniteReadMe" file that is in your Carbonite folder. The only thing I found was this:
The size, position and settings for the map are saved. These settings are also saved independently for each battleground.
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So, I'm really hoping if you choose to import a character setup with another character that all the BG map sizes are also imported. It's listed under the "-- Map" heading.
That "Punks" thing. It's my contention that all that is is a resource waste. I've had it turned on and have had it alerting me to "punks" that aren't even on the same continent I'm on. Example: I'm running around Durotar, and the "punks" thing is warning me that there is a "punk" near me ...... In Silverpine Forrest. Yeah. "Not good" doesn't even begin to cover it. Ever been to Ratchet? I've been standing right next to a Night Elf waiting for the boat to Booty Bay, yet I wasn't being alerted to any "punks" in my area. Hmmmm.... This happens just about every time I get the urge to try it out again. I just leave it "disabled" and go on my merry way. If I'm gonna get "ganked" somewhere, I'm gonna get "ganked".