Q: Icons missing from dock

What do you mean by "missing" - something must be there or you couldn't have "dragged them off the dock"??

Have you tried deleting the dock preferences and relaunching the dock?

charlie

Good!

Icons of DOCK items could be restored in Snow Leopard, but not in El Capitan.
But, in El Capitan, there is a small work-around. If you put an alias (or any other file) with the icon you want as the VERY FIRST file in that window (ex. if you always sort by name put a space as first character), the dock item will show that icon!

Hoping this might help.