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As long as you explain properly, tell them the truth and have proof it shouldn’t be a problem! There is nothing keeping you in Canada while they process your application, but you have to meet all the requirement to return.

But inland applications don’t need biometrics!
Yeah but My study visa is outland. Outland application requires biometrics.
 
I got the Acknowledgment of Receipt email on the 5th. Not the invitation as I wrote in my initial message.
Sorry I meant have you received an email for invitation on the 15th? And was it just he email or a letter? And was it sent to the sponsor?
 
Sorry I meant have you received an email for invitation on the 15th? And was it just he email or a letter? And was it sent to the sponsor?
Application sent: 11th of September
Acknowledgement of Receipt: 5th of November
Invitation to apply to MIDI Quebec: 15th of November
I received both via email to the sponsor. They also sent a letter to the address on file but letter arrived later than the email.