@ArcaneStudio I think this is a problem of UX clarity that needs to be improved with the “save as prefab” flow. What’s happening in the video is that when you select an existing instance of a prefab, then choose “save as prefab” on it, you end up creating a derived version of the first prefab.
Code wise this is the equivalent of:
base_prefab := class(entity):
Cone1
Cone2
derived_prefab := class(base_prefab):
Box
When you then remove the base prefab, your derived prefab no longer contains the values either, as they were always coming from the base.
Without some better UX around that this is definitely going to be a gotcha. We’ll keep improving this over time to add both clarity to what’s happening right now and alternative flows that would allow you to create entirely separate “deep clones” of the prefab instead, which appears to be what you were looking for.