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This similarly happen to me. I got an email saying my application status is updated on Aug 27, when i check my GCKey, it said application "approved". When I go inside it showed application is in progress, eligibility and Background check is still in progress. My biometric info disappeared. But i never gotten counterfoil generated. I submitted my passport and its still under progress since Aug 13. People from my date are already getting their passport stamped and dispatched already... did you happen to call them? if did, what they say about the changes?

Hey there. I came across your post. I know its an old thread but I am facing this similar situation as you had faced in the past. Do you by any chance remember how you resolved this issue? Whom did you contact?
 
Hey there. I came across your post. I know its an old thread but I am facing this similar situation as you had faced in the past. Do you by any chance remember how you resolved this issue? Whom did you contact?
Hi, facing same situation. How is yours now?
 
I think there was a technical problem with the IRCC system.
1st counterfoil became invalid and then they generated counterfoil again.
My wife got her passport back yesterday.
I tried to contact them but they were not able to transfer my call.
Biometrics is still removed from her GCKEY account so do not worry about it.
You can report this problem from GCKEY page. Also try to contact IRCC.
Good Luck

Hey hope you are well.

May I know kindly-how did you resolve your issue ?