How can I repair broken glass inside a stained glass project?
Take it apart

Desolder the near and far corners of the frame - easier said than done, but just patiently melt the solder and push it away with the tip of the soldering iron. 

Glue the broken glass back together

Once half the frame is removed, the broken pieces will probably still adhere to the foil, but still be flexible to allow the insertion of your favorite glass glue - e.g. Loctite.  Of course this does nothing about patching the missing shard of glass.

Place copper foil patches in the cracks

Once half the frame is removed, the broken pieces will have to be removed. If you're lucky the pieces of glass will slip off the foil.  If the foil continues to adhere to the glass, it might be necessary to peel off some of the solder coated foil and replace it.  As for filling in the cracks, the pieces will need to ground down so that cracks become wide enough to accommodate foil.  Foil the pieces, coat with solder on both sides of the piece, and reattach the frame pieces.

Do nothing 

Repairing with foil is going to look really klutzy. Using glue still leaves a gap where the chip of glass is missing, not much different from doing nothing.