Hello there, sorry to hear that. What you can do is apply for a "Restoration of Temporary Resident Status" even tho, when you apply for PR under the family class, you don't need to be in status, but if it brings peace of mind to you and your partner, you can apply for a restoration
You can go here:
http://www.cic.gc.ca/english/information/applications/visitor.asp
And open the IMM 5708 and then you click where it says "Restoration of Temporary Resident Status as a visitor"
Did you and your partner submit the PR application already?
When was he "supposed to leave Canada" ?