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Don't use MS-DOS scripts. I'd recommend PowerShell unless you have a specific need for VBScript, but either of those two will surface additional options in the script generation wizard, including the ability to specify an application that should run after the backup. So if you can distill your FTP command down to a single command line with arguments, you can just put that into the wizard. If not, that would probably still be a better foundation from which to build something custom. For one thing, PowerShell allows you to make the execution of post-backup applications conditional on whether the backup actually succeeded. And anything that can be called in Command Prompt can be called in PowerShell, possibly with some syntax tweaks.
Alternatively, if you can enable SMB on the Linux server (or Samba, as they call it), then you could potentially just use the Directory Synchronization option baked right into the script generation wizard. The easiest option of all would be to configure the backups to run under a Windows account with credentials that both have admin privileges on the local system AND have access to this Samba share you would create, in which case you wouldn't even need to hard code any authentication info into the script. The Directory Synchronization always causes the regular destination folder's Reflect backups to be mirrored to the synchronization target, which would include deleting files at the synchronization location that no longer exist at the regular backup destination. I would imagine something similar could be achieved via FTP though if necessary.
But no, Reflect does not return the name of the newly generated backup when it exits, so you wouldn't be able to use that as an input to something else later in the script. That's partially why folder mirroring as I described above can be useful, but if that isn't feasible, you could do something like checking the destination folder for an MRIMG file with a Creation Date within the last minute or something in order lock onto the correct file.