Yes you are right. Stage 1 is completed and they may or may not look at the new job credentials. I did have a change in my position within work and I emailed Ottawa the new documents like letter of reclassification, original job contract etc. Doesn't hurt to let them know you are better off now than you were before financially (if applicable) ... if anything it could act as a bonus for us!
CHC-Islamabad should add those documents as 'additional documents' to your electronic file. If not, our IMM0008 and other forms expire after a year anyways so we can (or our spouses) mention the updated job credentials on the new forms.