Auto FTP Manager allows you to overwrite the file on the destination if the size has changed.
First, you have to create an Automated profile from
File >> New Connection Profile. Select connection profile type as
Automated Profile.
On the next page, enter FTP details such as FTP address, port number, username and password. Navigate to the next page, look for
Action rules section and select the transfer actions. Set
Conflict resolution to
Overwrite if date/size is different. Click Next button, enter profile name and finish the settings.
Now, whenever you will start automated transfer, files on the destination will be replaced with files on the source if the size has changed.