[...] Of course a message after the encryption will improve the situation but my concern is that people will either ignore this message or they might misstake it in a way that they assume that their wallet is automatically safer now and they don't have to take care of old unencrypted backups (and delete them).
I think it's a valid concern that users might read the part of the message that says "[...]
previous backups of the unencrypted wallet file will become useless as soon as you start using the new, encrypted wallet." as meaning that the unencrypted backup is now of no use for a hacker if one were to get hold of it, instead of meaning that the backup cannot be relied upon as a replacement for the encrypted wallet.
The thing is, we need to convey both the following facts, without confusing the user too much:
1. The user cannot rely on the old, unencrypted backups as a replacement for the new, encrypted wallet file
2. At the same time, the old, unencrypted backup
can still contain keys that are in use with the encrypted wallet
I think the best solution, as has been mentioned, is simply to move over all coins, that are associated with the keys from the unencrypted backup, to a new key from the encrypted wallet. Would there be any problems in doing this (besides finding someone to implement it)?
How about changing the message to the following as step in the right direction for now?:
IMPORTANT: Any previous backups you have made of your wallet file should be replaced with the newly generated, encrypted wallet file. Backups made from the old, unencrypted wallet file cannot be relied upon as a replacement for the new, encrypted wallet. However, any backups of the old, unencrypted wallet file might contain sensitive information about addresses that are still in use, so it is important that they are removed from any unsafe storage locations. If you have not manually made backups of your wallet file before encrypting it, you can safely ignore this message.