Looks like a bug in the driver where markAsPartialObject is not set when querying with findOne(DBObject o, DBObject fields).
In effect a collection.save(object) causes loss of unselected fields.

This code illustrates the behavior (at least on my machine):

DBCollection col = new Mongo("localhost").getDB("test").getCollection("test");
col.drop();

// insert document with two fields:
DBObject t = BasicDBObjectBuilder.start("name", "marc").add("company", "viadesk").get();
col.save(t);

// prepare query and field selector:
DBObject q = BasicDBObjectBuilder.start("name", "marc").get();
DBObject f = BasicDBObjectBuilder.start("name", 1).get();

// call findOne to get object, returns full document:
DBObject r = col.findOne(q);
System.out.println("findOne (all fields):");
System.out.println(r);
System.out.println("isPartial: " + r.isPartialObject());
System.out.println();

// call findOne to get object, now with only 'name' field,
// notice isPartialObject returns false!
r = col.findOne(q, f);
System.out.println("findOne (selected fields):");
System.out.println(r);
System.out.println("isPartial: " + r.isPartialObject());
System.out.println();

// try to save the returned document, this should throw an
// IllegalArgumentException: can't save partial objects
// but is doesn't:
col.save(r);
System.out.println("saved document");
System.out.println();

// call findOne to get object, now the 'company' field gone
r = col.findOne(q);
System.out.println("findOne (all fields):");
System.out.println(r);
System.out.println("isPartial: " + r.isPartialObject());
System.out.println();