Fixing holes in glazed ceramic tile can be very tricky. This is a solution that may not be perfect but it will provide a big improvement to your situation. You will need some polyester resin, which is often used to repair car bodies. Mix up some of the resin and apply it to the holes in the tile making sure that you overfill the holes. As it dries but while it is still rubbery take a razor blade and trim off the excess resin. Take some 600 grit sandpaper and sand the resin smooth. Wet the sandpaper with a little water to make it work the best. Buy a porcelain touch up kit and mix up a batch of paint that is the right color and paint the patch. After the paint dries sand the spot one more time and you are done.
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