Just resume the torrents/start your torrent client. Once you resume seeding H&R flags will be neutralized.

If you've removed the torrent(s) from your client but still have the files then just re-download the .torrent from here.
If the client asks for save location, select the root folder where the file or folder is located and not the torrent folder itself.
Once added, your client should start a recheck of the files and start seeding automatically.
However, if it starts downloading again, then you've chosen the wrong directory!

If you have deleted the files as well, re-download them and seed.
If for some reason the torrent can't be downloaded then you can zap the flag using seedbonus points.
However, with each zap the "Zap cost" will increase by 50%. So this option is highly discouraged.

You can also clear them using H&R Coupons. Coupons can be used without any penalties.
Coupons are distributed at the start of each month according to user class.
It can also be gained through contribution.