MongoDB Replication initial sync fails with OplogStartMissing
How big is your oplog?

Could it be that the oplog is filling up and overwriting the operations since the sync started before the initial sync has finished?  If this is the case, the new secondary will never catch up. I had this error once before, but can’t recall the exact error now.

Check the oplog start / end points by using 

rs.printReplicationInfo()


If this is the case, either increase the oplog size or pause the application (if possible).

I’ll dig through an old ticket and check the error I had with a sync failing.