Should I use thinset or silicone to reattach shower tiles?
If you are going to regrout the pieces that came off, you should use thinset.

If you are going to grout with silicone, you could affix the loose tiles with silicone.  I don't like silicone for use in wet areas, once moisture gets behind it, the area never dries out.  With grout/thinset, moisture can escape.  Sealing grout is like using a moisture blocking/vapor permeable housewrap over your sheathing.