Hey there,
So I can tell you what causes that error. My mod maintains a list of every siphon that's constructed - and removes the siphon from this list when deconstructed. This is necessary so it can run the part that siphons ore out of the ore patches and into the siphon.
Mods, when they add or remove an entity (like a siphon) have an option to not inform other mods about this.
My mod has this code: script.on_event({defines.events.on_entity_died, defines.events.on_player_mined_entity, defines.events.on_robot_mined_entity, defines.events.script_raised_destroy}, siphonremoved)
But it looks like that mod you use has chosen not to inform other mods when it removes an entity. And thus that error.
There's not much I can do about that. But you can contact the other mod's author and ask him/her to have his mod inform other mods when entities are destroyed/removed.
FWIW, that mod will break more than just resource siphon. For any mod that tracks when entities are removed - it's going to cause problems.
Lastly, this goes the other way too. If that mod doesn't raise an event when it builds something, this mod won't know there's a new siphon and that it needs to receive ore dust.