Another problem with my coppers

They have started disappearing from my blacksmith. I have even gotten to the point of completely blocking off my portal with blocks, and then they all dissappear at once and are in the nether when I go there. Do I just have to make a different place for my portal? I wanted to keep it in the Smith near my home since my potion station is in my attic, so im hoping there is a way to fix this.