This issue is already fixed actually.
The problem wasn't just a simple missing .valid check. It seems simple, but the invalid entity error was just a symptom of a bigger problem. When a warp would occur, my mod would lose track of the hidden inserters it uses to move ammo around. Normally, I handle these entities script side, destroying them when their relevant turret dies or is picked up. The problem was that I didn't have a chance to destroy them properly before a warp, and they are indestructible, invisible, and inoperable. I could have just done a .valid check and made a new one if it was invalid, but that would mean the one that was warped would probably never get destroyed. Over time, this would lead to thousands of extra inserters eating up resources in the background.
My solution was a sort of garbage collection that runs every 5 minutes and looks for stray hidden inserters and their LuaObjects. That way I can just let the invalid ents go and make a new one without worrying about leaving a bunch of useless objects in my global table.
As for on_entity_cloned, I implemented it a while back when you mentioned it in another topic. For the moment, I believe our mods are fully compatible with one another.