Hi,
The decision to allow you to withdraw your application is with the visa office even though you have initiated it.
I recommend you send a Case Specific Enquiry + an email to the relevant visa office for your country/territory to explain that you had inadvertently/due to genuine oversight/you misread the visa refusal question in the TRV form..... that it was a genuine mistake, that you have informed IRCC of your own accord, etc etc.
You'll need to mention your study permit refusal in the CSE and email.
Your visa office for communication continues to remain the same one which is responsible for your country/territory even though you have applied online.
If you aren't in a hurry, you'll need to wait for the visa office to confirm that your application has been withdrawn/your file has been closed (this could take a few weeks).... then order GCMS Notes just to double check the comments against your file before you submit a new application
Cheers