Hey, @nicknacnoe.
You already summarized it pretty well. It’s a very common bug, and we don’t really have logs over it. I would highly encourage you to record your Empyrion gameplay in the background while playing. We have a guide on how to set it up here: Recording your gameplay in Empyrion
The best I can offer you is a one-time exception, based on your word. I’ll put the item in your inventory next time I notice you offline 
In the future, we would need a video, where the loss is visible.
While the bug probably can’t be outright avoided, you can most likely minimize it by frequently restarting your game. Especially before crafting important items.
And if you’re crafting an important item, make sure to look inside the constructor the moment it’s about to finish crafting (the moment where it would normally go from crafting to being put in your container).
You don’t need to record the entire crafting process; just the final moments.