What could cause an index wipeout?

This may happen if you have a bug in your indexing operations.
Adding a unique name for the temporary index on every reindexing task should resolve the issue.

However, running reindex and other types of operations that don't touch index settings in parallel should not cause the wipe of the index settings.

First, check your logs for setSettings operations or copySettings operations and look for overwrites. 
Then, check for re-indexing operations. If two re-indexing jobs are running at the same time, this may cause issues like the following: 

• Job A copies settings from the source index to the temporary index which creates a new temporary index (i.e. MyTempIndex)
• Job B copies settings from the source index to the temporary index with the same name (i.e. MyTempIndex)
• Job A adds records to the temporary index
• Job B adds records to the temporary index
• Job A renames the 'MyTempIndex' index to 'MyPermanentIndex', which overwrites the existing 'MyPermanentIndex' index with the temporary index MyTempIndex maintaining the original settings and records. 'MyTempIndex' index disappears once after this operation.
• Job B keeps adding records to the temporary index('MyTempIndex') expecting it still existed. This operation, however, creates a new temporary index ('MyTempIndex') without maintaining settings copied from the original index.
• Job B renames the 'MyTempIndex' index to 'MyPermanentIndex', which overwrites the existing 'MyPermanentIndex' index with the new temporary index without settings and records