The functions that upgrade/downgrade the metadata format of config.chunks entries should be executed either before or after a chunk operation. Otherwise, we could end up in the following situation:

• Chunk operation starts
• Chunk operation get chunk document(s) to operate with
• Upgrade/downgrade starts
• Upgrade/downgrade finishes
• Chunk operation commits

A possibility could be holding the ChunkOpLock while upgrading/downgrading config.chunks metadata.
Also, for chunk operations, the current chunk document should be get/modified under the same lock before committing (without relying on ChunkType arguments arriving from non-lock-guarded sections as it happens for example here).