What are prefab overrides?

Per-instance changes to a prefab in a scene or variant: a unique HP value, a different color, an extra component. Stored as delta from the base prefab.

Why do overrides get lost?

Common: editing a base prefab in Prefab Mode and clicking Apply All on a child — Unity reverts the parent’s override. Or restructuring the prefab hierarchy invalidates instance overrides.

Should I use variants?

Prefab Variants are the modern recommendation. They formalize override layers, making it explicit which fields differ from base. Cleaner than ad-hoc nested prefabs.

Fix: Unity Prefab Overrides Lost After Nested Edit

Quick answer: Use the Overrides dropdown to review changes before applying. Prefer Prefab Variants over deeply nested prefabs — variants make override layers explicit.

A team building an inventory of weapon prefabs: a base Sword prefab and variants (FlameSword, IceSword) with tweaked particle effects. Edit the base, click Apply, and FlameSword’s flame effect vanishes.

Review Before Applying

In Inspector, with a prefab instance selected, click the Overrides dropdown:

List shows every override on this instance.
“Revert All” restores everything to base — danger.
“Apply All” pushes overrides into base — also danger if you wanted them local.

Use per-item “Revert” / “Apply to base” to be surgical.

Prefab Variants

To make “FlameSword”:

Right-click Sword prefab → Create → Prefab Variant.
Open the variant. Modify the particle component to be flame.
Save. The variant inherits everything else from base.

Now editing base Sword propagates structural/behavioral changes; variant’s flame particle remains.

Avoid Deep Nesting

Nesting prefab instances inside prefabs can cause cascading override loss if any of the intermediate parents change structure. Two levels is usually safe; three or more becomes brittle.

Diff Tool

Window → Asset Management → Open Prefab Diff. Compare instance vs base; shows which fields differ. Verify before commits.

Source Control Note

Prefab .prefab files are YAML. Inspect diffs in git to see exactly what changed. Variants only list deltas; reading the diff is straightforward.

Verifying

Edit base Sword: change handle color. FlameSword: handle color updates (inherited), flame effect intact. Save base; reload scene; both variants render correctly.

“Variants are the contract: ‘here’s what differs from base’. Without them, overrides are accidents waiting to happen.”

For nested prefabs you can’t convert to variants, lock overrides via right-click → Lock Overrides — Unity then refuses to revert/apply unintentionally.