I lost the Joker shoulder piece for my Luna/Joker :lol
It's no biggie to me, though. Since I always have the Luna/Joker figure displayed so that the Luna's stretch arm is accentuated and the Joker half more obscured (That, and I've only ever had all 9 forms displayed at the same time like, once. So I could also just cannibalize one of the other Joker shoulders should I have too.

Thankfully the Yellow fist I lost was her default closed one, which I have 5 identical ones of (6 when I get Christmas) :lol

Are the girl fists identical ? I keep the girl parts in a Seperate container from boy parts. ( this sounded wrong )

The generic hands are from what I can tell (closed fist, sword/gun holding etc). They both had a few "exclusive" ones though.

lol

I just keep all of the parts in each characters boxes. I mean, I am going to be keeping the boxes, why not store each figure's pieces where they belong?

I used to throw the boxes away out of habit. Now I keep all my ranger parts in a power range samurai sand bucket I found at party city and the hands in Seperate hot wheel car display boxes. All my rider stuff is in a plastic shoeboxes

Only issue is how you can quickly run out of space for boxes...

Currently, I have two clear storage containers full of nothing but FIguarts boxes.

Yes, but the figures can be put back into them, and because they are imports, it makes keeping the boxes a must. It isn't like MOTUC, DCU, or Transformers where the boxes are pretty much worthless cardboard.

Plus, the boxes look nice spined and lined up on a bookshelf.

Invest in a Sterilite storage tub. Anything 25 Gallon and higher will solve all your storage needs.

Ive never seen a reason to throw away boxes for any of my Figuarts or DX Mecha. You automatically decrease their value if you do that. And they're incredibly handy to have if you ever wind up moving.