When handling database entities like accounts or characters I used to parse the BSON object, build the Java object from it, and then discard the BSON object except for the _id. When saving the entity, I used to build an entirely new BSON object with the same _id and the data of the Java object and saved it to MongoDB. The drawback of that approach was that any information in the database which was not parsed, stored and written back by the Java object was lost on updates.
To make it less likely to lose data this way, I decided to carry the original BSON object around in the Java object and overwrite all known values with the current ones on saving. That way any data the server does not read is retained.
This does, however, not totally prevent data loss. When a bug causes the server to suddenly be unable to read a value but it is still able to write it, it will replace it with a placeholder value. It also doesn't prevent data loss when the server screws up a dataset during gameplay.
In order to do some damage control in such a case, I could save every object not just to the main collection, but also to a separate backup collection with a non-unique key consisting of name and timestamp. This would give me the opportunity to roll-back individual characters to a previous point in time, should the need arise.
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