Restoring backup should have an option to disable Jira from sending and fetching email right after the backup has been restored.
The current Jira behavior is to fetch email from the configured boxes right after the restoration even if the DB restore failed! This obviously causes the system to actively destroy data since the emails are lost into the DB that was failed to be restored properly.
Workaround is to restore while the server is disconnected from the network but given that probably most administration of Jira instances is handled remotely, this is not very optimal.
Deleting / not restoring email settings is not an option either since the settings might be quite complex. I guess you'd need a global "turn off email" switch and make all email functionality honor that.