If items are in a crafting table, anvil, enchantment table or anything that isn't for storage, or the item is selected in the players' inventory, the items vanish at server restart. I've lost a stack of ores. This can irritate players and cause problems when crafting, etc.

Same thing happened to me

(yes, i know its from august but its still not fixed)

Hi,

so it’s not a glitch it’s part of the clear lag as items in crafting tables etc count as being entities at that point (same as if they were dropped) so the server clears them same as when lag removal occurs. This is why you get a 30 second warning to make sure you aren’t crafting it in an anvil when the server resets. 

Hope this helps!