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.
That sounds Perfect! Thanks so much for your timely help... i was stuck in this for a while and now i have some direction to go towards. Just one final question - i will be getting the letter from my manager only and i will get this notarized. In this case, do I still need to produce a letter of explanation with additional documents to prove my credibility? If yes, what are the documents should i include? I’m thinking about my recent payslips, Form 16, and my appointment letter and my appraisal letter too. Will this suffice?