Since there is now doubt that the balls were underinflated, the next step in the investigation must be to see if someone deliberately deflated the balls. Absent video evidence of someone deflating a ball, the whole matter will become a matter of he said, she said. The NFL should watch every minute of film covering the balls during the hours after inspection. If there is no evidence of intentional deflating, then the NFL should polygraph everyone from the ball boy to Robert Kraft. The results should be made public. This information will impact the value of the business commensurate with the level at which involvement is proven.
Of course, as usual, the NFL itself is primarily responsible for allowing this to happen. Regardless of the outcome, the NFL should simply not allow the teams to handle the balls except on the field. I am confident the balls can be manufactured to have a suitable surface.