Most shower doors are only siliconed on the outside (and along the wall channel). If you didn't silicone the tray first, you would have a hole at the bottom of the door frame.
When drilling through the tiles for the door frame, it might be a good idea to put some masking tape over the silicone. The red dust from ceramic tiles can stain the silicone.
Do you mean that the channel for the door frame is already in place? If yes, and you believe that the tray wasn't fully siliconed, you can use remove the channel screws and use a a flexible snap off blade knife to cut through the silicone behind the channel- personally I use my filling knives which, after years of sanding, are razor sharp.
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