Originally i had Reported this to the author of the Auto Deconstruct mod https://mods.factorio.com/mod/AutoDeconstruct as technically this is a bug with there mod but they have responded in the report https://mods.factorio.com/mod/AutoDeconstruct/discussion/687d49fdf44f47fa35235427 that they dont want have a whole bunch of extra code specificly for this mod due to how this mod implements the Omega Drill and i wanted to forward the suggestion they had made on how you should handle the deconstruct event, specifically "on_robot_pre_mined" to have the robots remove the chests content first and once its empty mark it for deconstruction or manually delete it via scripting to avoid errors.
The way how This mod currently handles deconstruction leads to the contents of the chest being deleted once the drill has depleted a resource deposit and a robot deconstructs the drill, wel technically this always happens regardless of the other mod and if its done by a robot or the player but using the Mod makes it a lot more obvious.
In my example it was only stone but it would probably really frustrating if the drill is used to mine some rare or valuable resource faster and then suddenly a chunk of the resources gained get deleted due to a scripting oversight.
