Forty-eight days is a period of time which is generally known as a mandala, a time period when the system goes through a certain cycle. This is also the reason why in Ayurveda for example, medicine is usually given for 48 days.
It is the length of time that is needed for the medicine to take root in your system. The same is true for the Isha Kriya. It is important that you do it without a break for that period.