FLR at Software Encryption => Use U-AIR to boot VM including encryption software and transport data over the network.
If encryption software support => mount the encrypted data on a second server with installed software you can use Instant VM Recovery to unmount volume and mount it as a additional drive to a server with installed encryption software.
If you see the encrypted disk as a file lying on a windows file system, you can use WinFRL to mapp the volume to the backup server and start (after installation) there the encryption software.
Or you can Share (windows share) it to a server that can mount it.
SQL Encryption is transparent to U-AIR SQL Wizard (because db data is online on production and U-AIR started DB.
At the moment we do not have Veeam Explorer for SQL, so it will be a feature requet for VESQL to mount encrypted SQL DBs as well.
But to be honest I haven´t seen a single MS SQL DB that is encrypted on DB level in the wild. Do you see this at other customers?