Quick answer: Serialize the full quest state, including step flags and counters, into the save and rehydrate the runtime quest objects from it on load.
If a quest forgets a step you completed after you reload, its flags are runtime-only and never saved. Include quest state in serialization. Here is the fix.
How to fix it
1. Serialize quest state
Write each active and completed quest's id, current step, and any counters into the save data, rather than leaving the quest object as transient runtime-only state.
2. Rehydrate quests on load
On load, rebuild the runtime quest objects from the saved state and restore their step and flags before any quest logic runs, so progress survives a reload.
3. Version the quest schema
Store a quest data version so that if you change a quest's steps in an update, you can migrate old saves instead of silently corrupting in-progress quests.
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.
Most of the time the fix is small. Seeing the failure clearly is the part that actually costs you.