I suppose you are the applicant and want to visit your family outside of Canada. Your application can be cancelled and not allowed to come back in until your PR application, which has to start from the scratch, is approved. If I were you, I would not leave Canada.
I crossed the border with my fiance (and yes we declared our relationship as such) he asked if I was planning on immigrating and I said yes and he sent me inside to immigration to recieve a VR. I am visa-exempt( US) but what this did was I was issued a UCI/Client ID on the paper stapled into my passport.
Yes you will most likely have a problem, as there's a strong chance you will be denied entry trying to return to Canada and have to cancel your entire application and start over. Applying inland, you need to be prepared to stay in Canada during the entire 1.5 years or however long it takes to complete the processing and get your PR. Unfortunately they don't make ANY allowances on leaving the country, no matter if its a serious family emergency or not. One of the biggest drawbacks of applying inland.