• I have a one member mongod instance (Server1) with a very large DB with 2.5 million documents (Each document is very big) and 4 indices.
• Then I added another machine (Server2)to this replica set. Mongod on Server2 takes about 5 hours to fetch all the documents in this big database.
• After all the documents are fetched by Server2, It starts making secondary indices. It takes around 3 hours for indices to get finished.
• Immediately after completing building the secondary indices, It tries to connect to primary and finds that socket is expired and timed out.
• At having received a timeout error it (Server2) simply drops all databases and starts the initial sync again.

Logs are attached as an image.