The test disk/repair_invalidates_replica_set_config.js calls in to wt_file_helper.js to wait for a repaired node to initial sync and become a secondary.
This uses waitForState(node, SECONDARY), which calls "replSetGetStatus" on the primary. If the primary is unaware a secondary was shut down, this will succeed, and the subsequent call to "replSetGetStatus" on the secondary will fail.
This should be replaced with a call to ReplSetTest.awaitSecondaryNodes(), which calls isMaster on each node to confirm its state, instead of just the primary.