So for anyone this has happened to, and you are concerned about your work permit, I just spoke to a rep from the IRCC on the phone.I also think they have already started processing OWP. Good luck
She said;
*they usually hold on to the open work permit application if its all correct and await the return of the rest of your application (for permanent residency, as they go hand in hand)
*BUT the lady checked my file, they usually leave a note saying that this is the case, but they did not. So what she told me to do is include a letter of explanation, payment receipt for the open work permit (as that wasnt sent back to me) and a copy of my current work permit (which expires june 24th 2018)
I've sent it off now, I'll let keep you updated if anyone is in a similar situation