YOu should be able to carefully cut "ALL" internally applied fillets on the panels including the bottom and reapply silicone and be just fine. I would not worry about the silicone between the glass edges....as your talking about paper thin area anyhow. Just make sure you use a good new sharp razor blade and remove any and all film of residual silicone from glass panels...even as scrub with the red colored scotch brite pads dampened in acetone or lac thinner will remove some of the film, but judicious use of a single edged razor scraper usually does a fine job of cleaning glass free of silicone. Silicone just does not stick to cured silicone, so unless all fillets are removed, and new is applied you run the risk of a leak, or having it lift and peel off.
Running a good filet of silicone in the inside corners and on the panels can be a nightmare for some folks all due to various degrees of experience. So if your not wanting to chance it, after you remove and clean the inside panels, use masking tape cut and run paralell to where the joints are. Basically outline all fillets with mashing tape. Apply a bead of silicone, and smooth out making sure it flows onto the masking tape and is feathered at that point. The tape will prevent yu geting a feather edge to "0" thickness which is most prone to pulling up, and also provide a guide to make the silicone in nice straight lines. Allow about 15 to 20 minutes setup and pull masking tape off pulling it off at an agle to the silicone, and you will be left with nice straight fillets of silicone that equals what any factory applied sealant job would look like if not better.
