I never tried Total Commander for FTP, but I know it can open 2 FTP panels.
I think every Windows user should have Total Commander as there main file management program.
At least all my friends and family I mentioned it too are now all also convinced users.
CloudBerry I do know for sure it can do what you want, done it myself. I do have the Pro version, but am not sure if the free version also does it. You can copy, move, delete any file between the same domain or different domain.
Please note that in principal you should always use SFTP (with a real FTP program like FileZilla - FREE) for all FTP operations/transfers, since SFTP encrypts all data incl. user/pwd. Using unsecure FTP could get your websites hacked. So use CloudBerry/Total Commander only for the cleanup, but not as a standard FTP program.