Repairing Content Index on DAG server can be easily done with Update-MailboxDatabaseCopy with switch -CatalogOnly.
But how to repair Content Index when there is no other DB copy?
Well, here is the great article:
On Exchange 2007 and Exchange 2010 there is ResetSearchIndex.ps1 script, which is placed in $exscript folder.
On Exchange 2013 there is no such script, so the only solution is to simply recreate the CI folder. To rename it/remove it, 2 services Microsoft Exchange Search and Microsoft Exchange Search Host Controller would need to be stopped.