When upgrading the Omega-Tau drill to a higher quality variant, a few things happen:
1. It cannot be upgraded in-place (you cannot place over the drill with a higher quality version, like you would with other machines)
2. If upgraded through an upgrade planner, the base drill itself is upgraded yet the drill storage is not replaced, causing two entities to occupy the same tile.
If the drill is removed after upgrading via upgrade planner, there is a ghost entity of the drill storage - unsure if it belongs to the drill that was replaced or the drill that replaced the old one. This ensures that no entity can interact with the storage of either drill, be it loaders or inserters.

I only tested this with the Omega-Tau drill in specific, not the normal Omega drill. Unsure if it affects that one.

Thank you for the report!

It affected both, and is now fixed. Although it's very bizarre that upgrading an entity raises the built event without raising any of the destroyed events.
As a side-effect, hand-upgrading from Omega to Omega-Tau is now possible.

Many thanks for the fix! :)