Some update on what's been going on.
After notifying through CSE, I got no response for an entire month. Finally, last week I sent a mail to cpc-ctd-ottawa@cic.gc.ca and then I copy pasted the same mail to delhi-im-enquiry@international.gc.ca
Remarkably, everything moved all at once within 24 hours or so
1. My spouse, who also has got an ITA and had applied individually under Federal Skilled Worked, has an application which had not moved forward since October. She got a mail saying her Application was updated. I checked and her application has moved to Background Check in progress.
2. CPC Ottawa replied outlining an 8 step process (Payment of Fees, Forms, Documents, PCC, Medical etc.) and gave us a 7 day deadline to get everything done and a decision would be made accordingly, and their mail mentions that my application can be rejected too.
3. Delhi Immigration replied too and as per them, both me and my spouse were meeting the standards individually and they advised us not to reopen our files. They said they had inserted a note into our files about our Marital Status changing and I could proceed with landing formalities and show the landing officer the mail they had sent.
As can be seen, the response from Delhi Immigration is very positive and the easiest way for us. However, my spouse has not been given a visa yet which I pointed out to them and also told them about the response we had received from CPC Ottawa which confused the issue.
CPC Ottawa seemingly did not consider the fact that I had pointed out that my spouse has also applied for PR individually, submitted documents, paid fees and everything. I sent them a mail for clarification but haven't had a response yet although they have had only 2 working days to respond.
I am now in a conundrum. Should we pay the fees (Processing+RPRF) a second time for my spouse? I have got all the documents and forms ready, but I am still waiting from a response from either of the id's for the clarification mails I sent.
I also don't know if there is any difference or benefits in getting PR for my spouse individually as a Federal Skilled Worker or is the Spouse visa just as good. Anybody want to shed light on this? Also, if we pay the fees again, would her application now start again as a Spouse PR application and will it take longer? I ask this because her individual application finally seems near completion. How long does it take for Background Check anyway? It would be great if someone could shed light on this.