Initial sync must copy in-progress index builds along with built indexes for two-phase index builds. v4.0 Index builds write a createIndexes oplog entry upon completion, which allows v4.0 initial sync to ignore in-progress index builds and instead rely on seeing the oplog entry during the oplog catch-up phase. Two-phase index builds, however, write oplog entries prior to completion that will not exist in the part of the oplog that initial sync reads during catch-up.