All income earned within the fund will be tax free in the pension stage, as you are both in pension stage. It will not impact the taxable / tax free ratio.
In your situation with rents coming in I would suggest you get the certificate done ASAP. Not sure how long you have to get one, and you may be safe. But as it has to occur before end of June anyway, why delay it? Better to have it in your hand so you have visibility of exactly where you stand with the % split.
