This is huge issue.
I ran reIndex on one of our collections and this was the output:
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.