Mongodb – what will happen if MongoDB primary host is down and secondary is out of sync. will we lose transaction

You need to change the config such that there is only one member remaining, and you have to do it on that host, i.e. Ubuntu12041vanilla:27017

The others are unreachable from its perspective, so even if you go with 2 nodes, 1 out of 2 down means you cannot form a majority and you will still only have secondary state.

Given your current rs.status() output, try this when connected via the mongo shell to Ubuntu12041vanilla:27017:

cfg = rs.conf()
cfg.members = [cfg.members[0]]
rs.reconfig(cfg, {force : true})

That will give you a config only one node and should mean that Ubuntu12041vanilla:27017 will be the only remaining member and primary.

Some time ago my one of my data replicas which was secondary at a time crushed due to hard drive failure. After I fixed that problem and restarted secondary it went into “Recovering” state. But my arbiter is now “Secondary”

A MongoDB arbiter cannot automatically become a secondary or a primary node, as it does not have a copy of the data set.

If you try to manually reconfigure the arbiter as a regular node via rs.reconfig() you should get an exception similar to:

{
    "errmsg" : "exception: arbiterOnly may not change for members",
    "code" : 13510,
    "ok" : 0
}

Furthermore, the data directory for this Arbiter shows bunch of files of total size >10GB. They indeed look to me like data files. Are they? What is going to happen to these files when Recovery completes?

Assuming this node is definitely an arbiter, I would expect those files are unused (check the timestamps?) and are either:

• a local database created if this node was incorrectly initialized with an oplog
• unused copy of data directory if this node was copied from another secondary or used as a standalone before

You can always log into the arbiter mongod directly to see what data it appears to have.