Hello sdesai,
I'm sorry to hear about your rejection. Since I went through the same stage, thought I'll share my two cents' worth with you. I was rejected in FSW at the second stage because I did the same mistake of taking the job responsibilities lightly. Like you, I also thought the onus of showing the NOC eligibility ended with Sidney, but I learned the hard way that was not the case. You can check my previous posts to see the details (believe it was in June/July of last year). I got the refund back rather quickly, I think after 3-4 months, but I got the IELTS back only last month, after numerous follow-ups with CHC via case-specific e-mails. I even offered to go there directly to collect it since I had to attend the Quebec interview in ND anyway (subsequently I got through that and am now waiting for visa stamping). They did not allow that. They did not return the transcripts or PCC saying it's their property now.
After my rejection, I tried to appeal giving detailed job description and responsibilities, a letter from my supervisor and payslips, but it seems once a rejection is made there is no revoking that decision. I feel you can apply by yourself since you have a pretty good idea where you went wrong, but this time leave no stone unturned. Get as much evidence as you can for the job - prove your job responsibilities, pay slips, job offer/contract, etc. - for the second stage, I mean. Since you got through to Sidney the first time, you can mention that you already got through there on (the date) and you were rejected at the second stage because you missed giving all available information to prove your experience.
Good luck!