1. If the chlorine cell is DOWNSTREAM of the filter, and all the pool water goes THROUGH the filter before it reaches the cell, then there won't be any debris reaching the cell.

2. If you are using a conventional start-up (pH between 6.8 and 8.0 at all times) and you turn the cell off during startup, you should be able to leave it in place.

Otherwise, you'll need to remove it.