Hi Martin,
I'm sorry to hear of the upgrade issues you are having.
Just to confirm - did you choose the upgrade existing installation option during the install? The data flows should be maintained when doing an upgrade rather than a clean install.
When restoring from a backup post-install (as opposed to re-importing the set of exported data flows) the 'executions' folder needs to be copied into the site\data folder, as described in Section 2, point 10 of the Dataverse Desktop Installation Guide.
Re. the JDBC driver, where was this installed on your system prior to the upgrade?
Thanks, Adrian