The 'config.system.indexBuilds' collection is replicated and the index build entries will be removed from it after the commitIndexBuild/abortIndexBuild oplog entry. However, this opens the possibility for these index build entries to be left behind in the collection. Consider the following sequence:

- Checkpoint @ 5.
- startIndexBuild @ 6.
- commitIndexBuild/abortIndexBuild @ 7.
- Remove config.system.indexBuilds entry @ 8.
- Take a backup. We will restore @ 5.
- Start a standalone on the backed-up files, set the oplogTruncateAfterPoint to 7.
- Restart with --recoverFromOplogAsStandalone.
- We replay the oplog entries at 6 and 7, but never 8.

This is already the case since v4.4 when aborting index builds and since SERVER-60753 when committing index builds. This doesn't have any bad consequences.