It won't raise eyebrows - you're allowed to edit the information in your application, even if it conflicts with your profile - in fact, you should. It is our responsibility to ensure everything we submit is accurate, even if that means having a discrepancy between your EE profile and your eAPR. A change won't have a negative impact on you unless the change results in your CRS Score dropping below the cut-off CRS for the Draw in which you received your ITA. The change you've outlined shouldn't have any impact on your CRS Score.
That being said, if your NOC Code is the same for both designations, I don't think you need to include a separate entry for your first designation. As I said, since both of my designations fell under the same NOC Code, I just included one entry for both of them.