No this is not possible. Cryptomator will detect an already running version and throw an error in the log.
At least as far as I know.
But did you read what the actual migration does? It’s basically nothing more than creating the new vault.Cryptomator file and editing the Masterkey file.
See here: Vault Format 8
This means, if anything goes wrong you can easily roll back. See here: [1.6.x] Downgrade to 1.5.x