Have you leak tested it like it is? For a sump that will be half empty, I am not sure I would start all over for that bubble. If it was a 40-50 gallon (or more) aquarium, then yes.
If you do decide to cut it apart, you need to make certain you get all traces of the old silicone off. Use a sharp razor blade to remove all of it and when you have it all off, use a brand new blade and go over the area again. Rub the surfaces where the old silicone was with acetone.
Use painters tape to mask off the areas you will be applying adhesive to give you a nice sharp edge.
You made a good choice with the RTV. If you ever tried to cut something apart that was put together with it, you will see the difference in holding power.