There are several possibilities and contributing factors.
If you're using card 2 for backup, then the image you're trying to delete lives on both cards and the delete probably just deleted the coy on card 1. Since you didn't delete it from card 2, it's still occupying space there and the camera probably takes the worst case of how much space is left on either card for its calculation.
Similar effect if you put jpegs on card 1 and raw on card 2.
As mentioned earlier, the camera makes a very conservative estimate based on the max space that each image could take. Since just about every image will take less than that, the size of the image you delete may not be enough to click the counter.
Two more points:
- I wouldn't worry about corruption of a card from deleting an image; that's an urban legend. Cards can and do get corrupted although very rarely. The solution is to use the second slot for backup.