Usually I make a backup of FDConnectionDefs.ini and restore it after updating. After my updates in the last years there was always a default FDConnectionDefs.ini without the Connections I added before.
Since this file is shared, even an existing D11 on the same machine does suffer from updating D12 in this case. In general I do not understand why the file is touched anyways - would be a great option in the update-options dialog to ask/inform customer about this overwriting of the file...