Well it was a bug, but i had to fix it abit different (well maybe a bug, but it was weird either way
)
I tried to cut the 4 amethysts i had mined out, but they were not on the list of my jc, i made another jc to see if they pop up, since they were in my stocks list, and i have seen them in their bin waiting to be cut. And well they were in the 2nd jc, but not the first, so i tried cutting them, but with the very first try, it gave me the message no amethyst available. Made a 2nd stockpile for only gems, and to take it from the bigger stockpile where other stuff get stored. But this time, the amethyst was removed from the 2nd jc aswell (the add new task list i mean). Dismantled and rebuild it, and they showed up again, but when i tried to cut them, poof they were gone.
After observations i made, is that the jc always lost the chance to cut the amethyst, whenever my succubus picked up the gem bin to grab another gem (basalt gems, still making them
). But once the gem bin was finally filled, and they started a new bin to pick it up, the amethyst could be cut, but before that, i checked the Well of souls, and the option to capture souls with gems was grey, before i even cut the amethyst.
It seems the thing that happend was that once a bin/barrel/pot gets grabbed, all the items in it, unless specifically used, disappear from the world, untill it get's put back into the stockpile.
I really hope that this long explanation can help you Boltbunny, aswell as any other modder/player that encounters it.