I don't think so. Typically I use CLR functions/procs in SQL Server when I must perform a certain task in SQL Server that cannot be easily done. One example was performing a regex search on data. This was quite a while ago so I'm not sure if there is a better way to do it now, but at the time a CLR function was a realistic option.
For your situation I would envision a .NET application that uses standard methods to access the databases, FTP stuff, and do whatever else. If you want to run that job daily you could setup a task in windows scheduler to run it.