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Hey there! Sorry about that! When you reloaded the game, your Runite was back though, I hope? If not, please let me know! I'm about to upload a version which saves the game after any shop purchase (I thought it did this already, but it does not). Currently, the best way to ensure a save is to simply Recall.
I agree, this limit is not the most logical thing in the world. The original thinking, was that it would encourage players to use a diversity of Runes. There is a Research to increase the max stack size, and it increases each NG+ as well. Overhauling the research and limits is on my todo list! :-)
 "Voxel Clicker")
 "Idle Empire 3")
 "Arcalona"){kind=icon}
 "TwoLands Clickers")
 "NOVA")
 "Stellar Squad")
 "Tabletop idle")
 "Paper Knight Quest")
 "Zombie Derby 2"){kind=icon}
 "Idle Mage Attack")
 "Steel Champions 2035")
 "Animation Throwdown")
 "Monster Looter"){kind=icon}
 "Battle For the Galaxy")
Fixed, thanks again