[Wally Arntzen]

Never, never use silicone as an adhesive for tile. Go to a tile shop and get the proper adhesive and scrape the floor clean for a good bond. Silicone is soft when fully cured and moves with weight which will cause the cracking.
Tuga just hit the cracked tile with a hammer in the center and take it out in peices. You do not have to take any other tiles out around the damaged ones.
If the tiles are larger than 4"x4" which I assume they are use a trowell with 1/4" notches when you put the tiles back on the floor. Often times I just trowel the mastic onto the tile itself and set in the space, that way you don't get all over the surrounding tiles.
I'm not a licensed tile setter but I am a contractor and have set thousands of square feet of different types of tile over the years.
I learned from the tile companies that I have use over the years as sub contractors.