Don't worry about it, Schengen visa tracking is even worse than that of the US and Canada. Once you get your Polish passport, just make sure to use it when your traveling in Schengen, and use the Canadian one when you go back to Canada. The Canadians don't care about not having an exit stamp, and the Europeans will never see the Canadian passport again.
z_darius: Since you are a Polish citizen I can't fathom how overstaying would apply to you. What are they gonna do? They can't throw you out of Poland. In Poland your Canadian citizenship will be of secondary importance - if any at all. The only thing on that is that if you are a Polish citizen, you must enter Poland with a Polish passport. But in reality, there are no real checks in place.
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