Each time one downloads from CRA's Auto-FIll, all available information is downloaded.

If you made changes to an amount after downloading the 1st time, when you download a 2nd time, that amount will be restored to the original amount from the CRA.

But, it doesn't clear out things you might have entered fresh.

For example, you download a slip that has an amount in box A but nothing in box B. You manually change the amount in box A and enter an amount in box B. When you download a 2nd time, the amount in box A will revert to what it was before you changed it but box B will stay as what you entered it, because there's no amount downloaded from the CRA to override it.