Quick answer: Persist a set of defeated unique-entity ids in the checkpoint and skip spawning or activating any entity whose id is in that set on load.
Beating a boss then reloading the last checkpoint should not bring it back. The checkpoint is not recording the kill. Persist defeated ids. Here is the fix.
How to fix it
1. Record defeated unique ids
When a unique entity such as a boss is defeated, add its stable id to a defeated set that is written into the checkpoint or save data.
2. Skip spawning defeated entities
On load, check each unique entity's id against the defeated set and skip spawning or activating it if it is present, so kills persist across reloads.
3. Persist related world changes
Save any side effects of the kill, such as opened doors or dropped rewards already collected, so reloading does not let the player farm a one-time encounter again.
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 Pygame 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.