Your BES instance name and your SRP ID need to be the same, other wise your service book on all the client devices will be incorrect and would not work again until they resynced or reran the Enterprise activation.
You could potentially do the new install with going straight to 4.0.4, but I would strongly recommend you create a backup of your database and know how to restore it back incase things go wrong. You can do everything right, but sometimes that database just won't upgrade properely.
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