Unconfirmed transactions are not guaranteed to be synchronized across all nodes (in fact, some nodes intentionally drop them sometimes).
In case your current balance was last altered (by value transactions) before the last snapshot, and all you did after that snapshot was to attach (unconfirmed) addresses, it could have happened that these addresses disappeared from the tangle as they were unconfirmed.
You noticed that you can regenerate and attach these regenerated transactions and the money comes back. You could also try to get these transactions confirmed (by reattaching/promoting) so that they cannot disappear again until the next snapshot.