I tried to use NBT Explorer, but that's just slow.

You can press G on an item, while hovering it in the creative tab.
You should join the discord server, if you have more questions :)

It is not working! realm.nbt is not updating, after Minecraft restart every removed item is back!

I'm not sure. It should work.
Make sure you don't have the file open in NBTExplorer at the same time, and I guess it also matters if you close Minecraft properly, rather than just closing the window

Not working. NBTExplorer is closed, the world saved, game closed with Quit Game button.

Hmm, I wonder what the issue could be... There might be an item causing issues, or if the file becomes too large.
Otherwise, I'm not sure what could be wrong. The saving works almost the same as vanilla hotbar saving.