erwin@ committed http://www.freebsd.org/cgi/query-pr.cgi?pr=149657, based on work by dougb@ and rene@. It deprecates the use of md5 checksums in distinfo. So here on in, when you run make makesum, the md5 will no longer be generated, only the sha256 checksum.
Existing distinfo containing md5 info will silently be ignored. So at this time there is no need re-create distinfo for the sake of removing it, just allow the regular flow of ports updates take care of it.