The test originally relied on the primary detecting an index inconsistency and aborting the index build from within the builder thread and replicating to the secondary. Which is why waitForIndexBuildToStop + awaitForReplication + assertIndexes guaranteed the assert on secondary would work. After graceful index builds, the secondary initiates an abort command on the primary, the index builder thread is killed, and the abort is external. So the above does not apply anymore.