ClodFlare WILL stop attacks against your FTP service. That’s the clue. If someone is attacking
your domain(!) on port 21, CloudFlare will not proxy the traffic (because it’s an unsupported port) and therefore it doesn’t reach your server.
But as far as i know, Battleflied servers are listed and published with their IP, not a domain name. But BF doens not need / support FTP?
It seems to me that something is mixed here.
Nitrado offers Webspace as well. This will be accessed via FTP to upload content. I found an article on their German Wiki pages how to change your domain to CloudFlare:
Not very extensive though.
They have also a DDoS mitigation in place. And they say, that they block the incoming traffic instead of sinkholing the target (like many other companies do). Not sure if this is true. Within your webinterface you will find a DDoS history. Is there any hint what exactly has been attacked?