What is the best and cost effective way to chip back tile away from toilet flange. I have to get little more room to add expandable flange

Hello, Installed corner shower (three piece plus doors). It is a higher end kit and the panels attach to each other with one inch flanges. Installation called for silicone in vertical joint (which was then bolted), silicone along bottom joint, and silicone on outside of door frame. So, essentially on continuous bead around all joints. This means there is silicone inside the joints almost acting like adhesive, and also on the surface of them, acting as waterproofing. Very difficult to do install, as the silicone was skinning before I could assemble the shower and smooth it all. Anyway, I got it done, but now it seems to be failing along bottom seam (door frame to base). My problem is how to repair. I know that new silicone doesn't stick to old, but there is no way I can get all of the old off. Some of the seams have silicone way back into them (i.e. one inch flange behind the joint) and short of disassembling the whole shower which is out of the question because the flanges are now tiled over. Can I just cut the superficial layer of silicone off, leaving the bit inside the seam and resilicone the surface? THe new silicone would attach to shower material at the edges of the bead, but the centre of the bead would be over old silicone and therefore I assume not sealed.