Quick answer: Export the properties you want saved, save the resource with ResourceSaver to a file, and ensure the resource keeps its script so it loads back as the right type.
A custom resource not saving is usually unexported properties or an unsaved file. Here is how to fix it.
How to fix it
1. Export the properties
Only @export (or otherwise marked) properties are serialized with the resource. Plain script variables are not saved. Export the data you want to persist.
2. Save with ResourceSaver
Persist the resource to a file with ResourceSaver.save (or save it as a .tres in the editor). A resource only held in memory is not written to disk and is lost when the game closes.
3. Keep the script reference
Ensure the saved resource retains its script (class) reference so it loads back as your custom type with its exported data, rather than a base Resource missing your properties.
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.
The bug you can't reproduce isn't gone — it's just invisible until you capture it from the player's device.