You won’t have to pay “back taxes”, but since you are preparing a tax return for Nova Scotia, then Nova Scotia tax rules apply. You may find that you have to pay additional tax on your employment income if Nova Scotia’s payroll taxes are higher than Ontario’s.
You also won’t be able to claim any Ontario benefits, like Trillium or LIFT, and Nova Scotia might not have any equivalents. So, your provincial taxes owing/refund may look different than what you are used to.