The gems I have in inventory are very unstable, and have disappeared on multiple occasions. (Playing on Android, version 1.0.17)
One major bug occurs when leveling gems using the gem temple candle quest received from the old man. Sometimes when level 8 gems raise to level 9, the new gems appear as additional items in inventory, instead of merging with the current stack of level 9 gems. When I exit and return to the game, only one of the level 9 stacks in inventory remains and the other has disappeared. This same bug occurs when using pandemonium tokens to raise all gems by one level.
But gems also disappear with no trigger or reason I can detect. On one occasion, while wandering the realms, I returned to discover 62 level 9 Nightmare Gargoyle gems (unenchanted) had simply vanished from inventory. I have lost more than 30 gems for my current project, a Mutant Spinewhipper, once in a clump of thirteen simply gone. Today I returned from the realms to find my level 9 diamond Mutant Spinewhipper gems had shrunk inexplicably from 10 gems to 9. This source of frustration is beginning to ruin the game for me, a game I otherwise enjoy.