Might be a very old bug, but when you pick up a backpack with bundled supplies in it, they usually are invisible unless you click twice to reveal them.
There's also a tool bug with it's durability invisible till you pick it up, besides that you can't just scroll and loot/transfer those items into your main inventory if it's in that state.
This stuff also may happen when those items are in chester.
1. Put tools/bundled supplies in chester/backpack
2. log off or stay away from those items for a while then come back to them later