It depends if you're using CompactLogix or ControlLogix. In CompactLogix (at least the ones I use) you can't reconfigure the analog cards from within the program. You have to configre them off-line and then download the program. At startup the cards are configured and ready for use.
I've read it's not the same for ControlLogix, but I've never used those yet.
The CompactLogix ones that I used can be configured online - you just have to do the configuration, inhibit the card (from the explorer) and the uninhibit the card. That makes the processor download the config info to the card again. You might want to give that a try with your CompactLogix cards.