This is huge issue.

I ran reIndex on one of our collections and this was the output:

{ 
        "nIndexesWas" : 2, 
        "msg" : "indexes dropped for collection", 
        "errmsg" : "exception: no index name specified", 
        "code" : 12523, 
        "ok" : 0 
} 

After doing this and calling getIndexes and empty list is returned. Our indexes are indeed gone.

Luckily we ran this on a secondary machine, but this is a huge problem.

This issue does not affect reindexing on a primary. Of course one typically does not reindex on a primary.

Workaround: Start the target mongod without "--replSet" and on a different port, reindex, and then restart mongod again with its normal --replSet command line. Be sure to use a different port number so no traffic other than administrative hits the machine during this maintenace procedure.