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I can't speak to the lates, but I would not be surprised to see a nice bump if I understood that it was reported late for 3 years. The card should give you a decent bump if you have not done any credit since you started making your trustee payments. I did not do anything while in re-payment and did not use any credit for a year after completion. A card just like you have brought mine up right in line with the simulator for about 43 points. My wife got a 53 point bump in hers across the board.
Once you have completed the agreed debt repayment under your Chpt 13, the debt balance will be updated to show $0.
Since it is revolving debt, that will effect your % util scoring, which is the basis for the score increase.
When it is "zeroed out," it will then show a $0 balance, so yes, the effect on your % util scoring will be the same.