We received this in an email from a CIC agent regarding the same. You still need to apply to extend the work permit, but apply using paper method only, and write that you have applied for PR across the top:
Open Work Permit – Sponsorship of a Spouse or Common-Law Partner in Canada
If a spouse or common-law partner is sponsored from inside Canada, they can apply for an open work permit by completing an Application to Change Conditions or Extend Your Stay in Canada as a Worker (IMM 5553). This application must be sent before their status expires in the same envelope as the sponsorship application. This will allow them to keep a legal status in Canada up until the time their application for permanent residence is *approved in principle.
If their status expires before the application for permanent residence is approved in principle, they will still have a legal status in Canada. This is called implied status. Please note that the open work permit will only be issued once the application for permanent residence is approved in principle. Visit our Web site to see how long it may take to get approval in principle.
If the sponsored person did not send an open work permit application with their permanent residence application, they can send it, by mail, at any time while it is in process by writing Open Work Permit - Application for permanent residence in Canada - Spouse or common-law partner on the top of the form. They should also include proof that the permanent residence application was submitted. The open work permit application cannot be submitted online.
Please note that they must keep a legal status in Canada during the entire process of their application for permanent residence.
*Approved in principle means that the person being sponsored received a letter from the Case Processing Centre or local office stating that they meet the eligibility (minimum) requirements to apply for permanent resident status but that a final decision will not be made until all requirements for becoming a permanent resident have been met. These requirements include medical, security and background checks for the applicant and, if applicable, their family members.