Quick answer: Unity Apply All on a base prefab erasing overrides on nested instances? Apply All propagates the current state - nested instances inherit the new base, losing per-instance tweaks.
Base 'Enemy' prefab. Variant 'GoblinElite' overrides hp = 200. Edit base, click Apply All; GoblinElite reverts to base hp.
Apply individual overrides
Right-click each modified property > Apply to Prefab. Targets only the property; preserves overrides on others.
Use Overrides > Apply Selected
The Overrides dropdown lets you cherry-pick which changes propagate. Bulk-apply is convenient and destructive.
Or use ScriptableObject for variants
If 'GoblinElite' is mostly data, an SO with the variant's overrides is more refactor-safe than a prefab variant.
“Apply All is bulk. Bulk operations need bulk care.”
For complex prefab hierarchies, lock Apply All behind a confirmation step in your tools. Junior engineers will appreciate it.