The 'save config' should work rather than the 'download config'. If Vemstune is communicating with the ECU and doesnt throw up any warnings, it should be fine. I upgraded from 1.1.47 without any issues. Vemstune should still see the ECU and allow you to save the config
You need to save config in Vemstune first, before uploading new firmware. The old Megatune config files are not compatable.
If you are trying to upload a Megatune config file with Vemstune after uploading the new firmaware, the only way I can see to fix this is to upload 1.1.44 firmware the old way, upload the config the old way, and then use Vemstune to save config, then upload the new firmware and then the config.
You shouldn't have too many problems with the config if its done this way, but you will have to double check everything and i mean everything, as there are so many differences, some of them still need manual configuring afterwards