I appreciate the situation you are in but unfortunately it is just a part of steemit. Part of being a decentralized platform means that there really isn't anyone in charge, its up to the community to police itself. Everyone has the right to vote their stake up or down for whatever reason they see fit.
Steemcleaners can help in cases of plagiarism, identity theft, etc.. and other things laid out in the Abuse Guide but we can't do anything about flagging wars. People choose to flag for any number of reasons, disagreement about rewards, plagiarism, or just out of spite. Your best bet would be to talk to the person and see if you can figure out why they are flagging you and if you guys can work it out.
Other options would be to write a post about what is going on and sway community support to your side, gaining some upvotes and restoring your rep. You can always power up more steem (not an option for everyone, I know) to the point where you have more SP than he does and you don't have to worry about his flags anymore. Sorry I can't be of more help, hopefully you are able to get things worked out.
Understandable.. I believe the situation has been resolved. Thank you for your advice.