How to safely remove a mod from an existing Minecraft world

Back up the world first

Not advice — a prerequisite. Some of what follows is irreversible, and you will not get a second prompt. Copy the whole world folder somewhere else before you start.

What happens when you pull a mod

The world stores blocks and items by ID. Remove the mod and those IDs resolve to nothing. On next load you get:

Unknown registry entries
Missing registry entries

and a prompt asking whether to continue. Saying yes permanently deletes every block and item from that mod out of the world. See the full write-up.

Do this before removing it

1. Find out what it still owns. Blocks placed, items in chests, entities, and — easily forgotten — items inside other mods' machines and backpacks.
2. Break down anything of value in-game first, while the mod still works. Machines holding items will take their contents with them.
3. Check what depends on it. Another mod requiring it as a hard dependency will refuse to start; see missing dependencies.
4. Check your scripts and quests. Every recipe, tag and reward referencing the removed mod becomes a silent no-op — see silent ID failures.

Chunk corruption is mostly a myth, with one exception

Removing a mod that adds blocks and items is usually survivable: the entries vanish and the world loads. The real risk is mods that add worldgen — dimensions, biomes, structures. Those leave chunk data the game can no longer interpret, and the boundary between generated and newly-generated terrain can be abrupt and permanent.

A mod that adds a dimension is close to unremovable from a world you care about. Treat that as a decision made at pack-creation time.

If the server will not start afterwards

Put the mod back. The world loads again, and you can do the preparation above properly. This is the main reason to back up before the first attempt — restoring is instant, undoing a registry wipe is not.

Doing this automatically

Forge Server Doctor performs the whole procedure above — reads the report, finds the real cause under the wrappers, skips the vanilla frames, and names the mod jar. 24 failure modes, each with its fix. The free edition covers the six most common startup failures.