his has happend me ALOT of times and im sick and tired of stacks of emeralds disappearing every time, this has happend to me last 3 months but i waited and thought it would stop. I dont know if its supposed to be that way but it didnt happen to me ever before.
well they'll not know what's creating the problem if you don't explain it, so tell them what your doing till it happens occur to they can find it easier as it might be something they not see and be able to be fixed as they're no idea what too look for.
Try, double clicking the inventory spot it was on. If not try placing a item where it was in you're inventory. If not re-start mc. Look to see if they are still gone. Contact a Admin + @NESlover
Emeralds won't go into your inventory if there are no available slots, also the only time emeralds leave you inventory is if you log while in combat never.