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Hi,

I filed the paper application but before it could be approved, got the PR Application approved for my son.

You can try raising the webform to check if paper applications are processed/not as in my case I never received a confirmation or acknowledgement of my paper application from Ottawa office.
 
The Visitor record matches my PGWP. I can apply online for myself from inside (or outside) Canada. For my wife and daughter, I can apply online only from outside Canada (I tried the new portal and it will let me apply but as if I am applying from outside Canada).
I am also on same boat,Did your daughter and spouse got the visitor visa based on the visitor record inside the canada? Please reply