I would firstly question the sealant used. Sanitary or glazing silicon isn't recommended. There are mastics available that can be applied in the wet but it's always better in the dry. I personally use Weathermate alot and have rarely been disappointed. If the gap appears to be too big for sealant alone to be appropriate, you can bridge the gap with an offcut of plastic guttering or even lead. Just seal the offcut with Weathermate or lead with Leadmate and it should hold.
scarywalton
November 2007