Quick answer: Either save the sub-resources to their own stable files and reference them, or use FLAG_BUNDLE_RESOURCES so they are embedded directly in the main save.
A saved Resource can store sub-resources either as external file links or embedded. If the linked file is gone, the property loads as null. Bundle them or pin their paths.
How to fix it
1. Decide embedded vs external
Embedded sub-resources travel inside the main file; external ones are links to separate files. Mixing them up is what produces null references after load.
2. Bundle when self-contained saves matter
Pass ResourceSaver.FLAG_BUNDLE_RESOURCES so sub-resources are written into the same file, guaranteeing they load together with the parent.
3. Pin external paths otherwise
If you keep sub-resources external for sharing, save them to stable user:// paths and never move them, so the parent's references stay valid.
Catching the ones you can't reproduce
The hardest version of this to fix is the one you can't reproduce — it only happens on a player's hardware, OS, driver, or save state, under conditions that simply aren't present on your machine. A report that says “it crashed” or “it froze” gives you nothing to act on, so the bug survives release after release while quietly costing you players.
Automatic error capture closes that gap. Each failure arrives with its full stack trace, the device and OS, the build number, and a breadcrumb trail of what the player did right before it broke, so even a failure you have never seen becomes a specific, reproducible issue. Fold identical failures into one signature ranked by how many players each hits, and your worklist sorts itself worst-first instead of arriving as a stream of vague complaints.
This is where a tool like Bugnet earns its place. Its SDK captures every Godot error automatically with the full stack trace plus device, OS, memory, build, and game-state context, folds duplicates into one grouped issue with an occurrence count, and ties each to the build it first appeared on — so you fix the problem that hurts the most players first and confirm it is gone when its signature disappears from the next release.
Ship the fix, watch the signature disappear from the next build. That's how you know it's really gone.