Quick answer: Split player-writable settings from read-only authored content into separate files with separate lifecycles, and never ship over the user's settings file.
Your update shipped new content but wiped everyone's keybindings, because both lived in config.json. Settings the player edits and content you author have opposite lifecycles. Separate them.
How to fix it
1. Separate the files
Put authored, read-only content in one location you ship and overwrite, and user settings in a separate writable file under the user data directory you never overwrite on update.
2. Use the right storage location
Write settings to the platform's persistent user path, not next to the executable or game data, so updates and reinstalls leave them intact.
3. Merge, do not replace
If settings must gain new keys on update, merge defaults into the existing user file rather than replacing it, preserving the player's existing choices.
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 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.
A crash you can name from its stack trace is a crash you can usually fix in minutes.