I'm not sure what you mean.
The ItemCollection are serialized, and like any serialized value the prefab instance checks if any value was overriden and if it was then it won't inherit i anymore. If not it will inherit its "original" prefab value.
That being said I'm not using Inventories of prefab variants personally. I'm not sure what your use case is but perhaps if this is causing you issues there might be better alternatives, like a list of ItemDefinitions. Or having another Inventory somewhere else and send the items back and forth, etc... It really depends on your use case