When using the Send to Bottom Of -> function sometimes cards disappear when this function is used. Not every time but about 40-50% of the time it seems to happen.
Is this happening with multiple plugins for you or one particular plugin? What build (Windows, Mac, Ipad)?
Windows and mainly when playing Raw Deal.
I've also been having this problem with my personal LCG, it comes up often enough because anti-mill is meant to be something you can build your deck around. There are literally fieldstates where you can return cards from your discard to the bottom of deck every turn. Forgetting card positions in a TCG seems like a really core issue with the engine that Trevor should fix. I've also noticed issues with trying to put cards back in specific positions (Scry effects).